From 7c7d4627b3144ac78ed8e5ca9d23cee445442dd0 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Wed, 6 Feb 2019 14:31:04 -0500
Subject: [PATCH 01/28] updated nipype2boutiques to conform to current schema,
 added default value for tool-version when interface version is null

---
 nipype/utils/nipype2boutiques.py            | 36 ++++++++++++---------
 nipype/utils/tests/test_nipype2boutiques.py |  5 +--
 2 files changed, 23 insertions(+), 18 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 21ecbc0eee..617a5d28d2 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -25,15 +25,18 @@
 
 
 def generate_boutiques_descriptor(
-        module, interface_name, ignored_template_inputs, docker_image,
-        docker_index, verbose, ignore_template_numbers):
+        module, interface_name, ignored_template_inputs, container_image,
+        container_index, container_type, verbose, ignore_template_numbers):
     '''
     Returns a JSON string containing a JSON Boutiques description of a Nipype interface.
     Arguments:
     * module: module where the Nipype interface is declared.
-    * interface: Nipype interface.
+    * interface_name: name of Nipype interface.
     * ignored_template_inputs: a list of input names that should be ignored in the generation of output path templates.
     * ignore_template_numbers: True if numbers must be ignored in output path creations.
+    * container_image: name of the container image where the tool is installed
+    * container_index: optional index where the image is available
+    * container_type: type of container image (Docker or Singularity)
     '''
 
     if not module:
@@ -59,13 +62,15 @@ def generate_boutiques_descriptor(
     tool_desc[
         'description'] = interface_name + ", as implemented in Nipype (module: " + module_name + ", interface: " + interface_name + ")."
     tool_desc['inputs'] = []
-    tool_desc['outputs'] = []
-    tool_desc['tool-version'] = interface.version
-    tool_desc['schema-version'] = '0.2-snapshot'
-    if docker_image:
-        tool_desc['docker-image'] = docker_image
-    if docker_index:
-        tool_desc['docker-index'] = docker_index
+    tool_desc['output-files'] = []
+    tool_desc['tool-version'] = interface.version if interface.version is not None else 'undefined'
+    tool_desc['schema-version'] = '0.5'
+    if container_image:
+        tool_desc['container-image'] = {}
+        tool_desc['container-image']['image'] = container_image
+        tool_desc['container-image']['type'] = container_type
+        if container_index:
+            tool_desc['container-image']['index'] = container_index
 
     # Generates tool inputs
     for name, spec in sorted(interface.inputs.traits(transient=None).items()):
@@ -73,7 +78,7 @@ def generate_boutiques_descriptor(
                                     ignored_template_inputs, verbose,
                                     ignore_template_numbers)
         tool_desc['inputs'].append(input)
-        tool_desc['command-line'] += input['command-line-key'] + " "
+        tool_desc['command-line'] += input['value-key'] + " "
         if verbose:
             print("-> Adding input " + input['name'])
 
@@ -82,13 +87,13 @@ def generate_boutiques_descriptor(
         output = get_boutiques_output(name, interface, tool_desc['inputs'],
                                       verbose)
         if output['path-template'] != "":
-            tool_desc['outputs'].append(output)
+            tool_desc['output-files'].append(output)
             if verbose:
                 print("-> Adding output " + output['name'])
         elif verbose:
             print("xx Skipping output " + output['name'] +
                   " with no path template.")
-    if tool_desc['outputs'] == []:
+    if tool_desc['output-files'] == []:
         raise Exception("Tool has no output.")
 
     # Removes all temporary values from inputs (otherwise they will
@@ -125,7 +130,7 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     input['name'] = input_name.replace('_', ' ').capitalize()
     input['type'] = get_type_from_spec_info(spec_info)
     input['list'] = is_list(spec_info)
-    input['command-line-key'] = "[" + input_name.upper(
+    input['value-key'] = "[" + input_name.upper(
     ) + "]"  # assumes that input names are unique
     input['command-line-flag'] = ("--%s" % input_name + " ").strip()
     input['tempvalue'] = None
@@ -178,7 +183,6 @@ def get_boutiques_output(name, interface, tool_inputs, verbose=False):
     output = {}
     output['name'] = name.replace('_', ' ').capitalize()
     output['id'] = name
-    output['type'] = "File"
     output['path-template'] = ""
     output[
         'optional'] = True  # no real way to determine if an output is always produced, regardless of the input values.
@@ -201,7 +205,7 @@ def get_boutiques_output(name, interface, tool_inputs, verbose=False):
             if str(input_value) in output_value:
                 output_value = os.path.basename(
                     output_value.replace(input_value,
-                                         input['command-line-key'])
+                                         input['value-key'])
                 )  # FIXME: this only works if output is written in the current directory
         output['path-template'] = os.path.basename(output_value)
     return output
diff --git a/nipype/utils/tests/test_nipype2boutiques.py b/nipype/utils/tests/test_nipype2boutiques.py
index f1d0c46eed..3aecefda63 100644
--- a/nipype/utils/tests/test_nipype2boutiques.py
+++ b/nipype/utils/tests/test_nipype2boutiques.py
@@ -11,7 +11,8 @@ def test_generate():
     generate_boutiques_descriptor(module='nipype.interfaces.ants.registration',
                                   interface_name='ANTS',
                                   ignored_template_inputs=(),
-                                  docker_image=None,
-                                  docker_index=None,
+                                  container_image=None,
+                                  container_index=None,
+                                  container_type=None,
                                   verbose=False,
                                   ignore_template_numbers=False)

From fc27d01227127f1c61033e72c4922afdd1b03368 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Wed, 6 Feb 2019 15:56:10 -0500
Subject: [PATCH 02/28] added a step to make sure output IDs are unique in case
 output name is the same as an input name

---
 nipype/utils/nipype2boutiques.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 617a5d28d2..626cf13067 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -182,7 +182,16 @@ def get_boutiques_output(name, interface, tool_inputs, verbose=False):
     """
     output = {}
     output['name'] = name.replace('_', ' ').capitalize()
-    output['id'] = name
+
+    # Check if the output name was already used as an input name
+    # If so, append '_outfile' to the end of the ID
+    unique_id = True
+    for inp in tool_inputs:
+        if inp['id'] == name:
+            unique_id = False
+            break
+    output['id'] = name if unique_id else name + '_outfile'
+
     output['path-template'] = ""
     output[
         'optional'] = True  # no real way to determine if an output is always produced, regardless of the input values.

From e7739e74c1fc78efa6603fa09b510069b33be544 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Thu, 7 Feb 2019 16:55:36 -0500
Subject: [PATCH 03/28] descriptor gets saved to a file for easier exporting,
 added value-choices extraction, added method to get input type from handler
 type

---
 nipype/utils/nipype2boutiques.py | 39 +++++++++++++++++++++++++++++---
 1 file changed, 36 insertions(+), 3 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 626cf13067..33eaeb56c1 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -101,6 +101,10 @@ def generate_boutiques_descriptor(
     for input in tool_desc['inputs']:
         del input['tempvalue']
 
+    # Save descriptor to a file
+    with open(interface_name + '.json', 'w') as outfile:
+        json.dump(tool_desc, outfile)
+
     return json.dumps(tool_desc, indent=4, separators=(',', ': '))
 
 
@@ -128,7 +132,10 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     input = {}
     input['id'] = input_name
     input['name'] = input_name.replace('_', ' ').capitalize()
-    input['type'] = get_type_from_spec_info(spec_info)
+
+    # Figure out the input type from its handler type
+    input['type'] = get_type_from_handler_type(spec.handler)
+
     input['list'] = is_list(spec_info)
     input['value-key'] = "[" + input_name.upper(
     ) + "]"  # assumes that input names are unique
@@ -145,6 +152,14 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     if spec.usedefault:
         input['default-value'] = spec.default_value()[1]
 
+    try:
+        value_choices = spec.handler.values
+    except AttributeError:
+        pass
+    else:
+        if value_choices is not None:
+            input['value-choices'] = value_choices
+
     # Create unique, temporary value.
     temp_value = must_generate_value(input_name, input['type'],
                                      ignored_template_inputs, spec_info, spec,
@@ -158,9 +173,9 @@ def get_boutiques_input(inputs, interface, input_name, spec,
                   str(tempvalue))
 
     # Now that temp values have been generated, set Boolean types to
-    # Number (there is no Boolean type in Boutiques)
+    # Flag (there is no Boolean type in Boutiques)
     if input['type'] == "Boolean":
-        input['type'] = "Number"
+        input['type'] = "Flag"
 
     return input
 
@@ -217,9 +232,16 @@ def get_boutiques_output(name, interface, tool_inputs, verbose=False):
                                          input['value-key'])
                 )  # FIXME: this only works if output is written in the current directory
         output['path-template'] = os.path.basename(output_value)
+
+    if not output_value:
+        # Look for an input with the same name and use this as the path template
+        for input in tool_inputs:
+            if input['id'] == name:
+                output['path-template'] = input['value-key']
     return output
 
 
+# TODO remove this once we know get_type_from_handler_type works well
 def get_type_from_spec_info(spec_info):
     '''
     Returns an input type from the spec info. There must be a better
@@ -235,6 +257,17 @@ def get_type_from_spec_info(spec_info):
     return "String"
 
 
+def get_type_from_handler_type(handler):
+    handler_type = type(handler).__name__
+    if handler_type == "File" or handler_type == "Directory":
+        return "File"
+    elif handler_type == "Int" or handler_type == "Float":
+        return "Number"
+    elif handler_type == "Bool":
+        return "Flag"
+    else:
+        return "String"
+
 def is_list(spec_info):
     '''
     Returns True if the spec info looks like it describes a list

From 181c481e003410e7e3f95156eaf04a1a0668c084 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Thu, 7 Feb 2019 18:16:59 -0500
Subject: [PATCH 04/28] added warning message when cannot determine path
 template for output, added check for integer types, added method to get
 description from spec

---
 nipype/utils/nipype2boutiques.py | 66 +++++++++++++++++++++++++-------
 1 file changed, 52 insertions(+), 14 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 33eaeb56c1..83148fc10f 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -63,7 +63,7 @@ def generate_boutiques_descriptor(
         'description'] = interface_name + ", as implemented in Nipype (module: " + module_name + ", interface: " + interface_name + ")."
     tool_desc['inputs'] = []
     tool_desc['output-files'] = []
-    tool_desc['tool-version'] = interface.version if interface.version is not None else 'undefined'
+    tool_desc['tool-version'] = interface.version if interface.version is not None else "No version provided."
     tool_desc['schema-version'] = '0.5'
     if container_image:
         tool_desc['container-image'] = {}
@@ -84,7 +84,7 @@ def generate_boutiques_descriptor(
 
     # Generates tool outputs
     for name, spec in sorted(outputs.traits(transient=None).items()):
-        output = get_boutiques_output(name, interface, tool_desc['inputs'],
+        output = get_boutiques_output(outputs, name, spec, interface, tool_desc['inputs'],
                                       verbose)
         if output['path-template'] != "":
             tool_desc['output-files'].append(output)
@@ -105,6 +105,8 @@ def generate_boutiques_descriptor(
     with open(interface_name + '.json', 'w') as outfile:
         json.dump(tool_desc, outfile)
 
+    print("NOTE: Descriptors produced by this script may not entirely conform to the Nipype interface "
+          "specs. Please check that the descriptor is correct before using it.")
     return json.dumps(tool_desc, indent=4, separators=(',', ': '))
 
 
@@ -125,8 +127,6 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     Assumes that:
       * Input names are unique.
     """
-    if not spec.desc:
-        spec.desc = "No description provided."
     spec_info = spec.full_info(inputs, input_name, None)
 
     input = {}
@@ -134,17 +134,17 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     input['name'] = input_name.replace('_', ' ').capitalize()
 
     # Figure out the input type from its handler type
-    input['type'] = get_type_from_handler_type(spec.handler)
+    input_type = get_type_from_handler_type(spec.handler)
+    input['type'] = input_type[0]
+    if input_type[1]:
+        input['integer'] = True
 
     input['list'] = is_list(spec_info)
     input['value-key'] = "[" + input_name.upper(
     ) + "]"  # assumes that input names are unique
     input['command-line-flag'] = ("--%s" % input_name + " ").strip()
     input['tempvalue'] = None
-    input['description'] = spec_info.capitalize(
-    ) + ". " + spec.desc.capitalize()
-    if not input['description'].endswith('.'):
-        input['description'] += '.'
+    input['description'] = get_description_from_spec(inputs, input_name, spec)
     if not (hasattr(spec, "mandatory") and spec.mandatory):
         input['optional'] = True
     else:
@@ -180,12 +180,14 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     return input
 
 
-def get_boutiques_output(name, interface, tool_inputs, verbose=False):
+def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=False):
     """
     Returns a dictionary containing the Boutiques output corresponding to a Nipype output.
 
     Args:
+      * outputs: outputs of the Nipype interface.
       * name: name of the Nipype output.
+      * spec: Nipype output spec.
       * interface: Nipype interface.
       * tool_inputs: list of tool inputs (as produced by method get_boutiques_input).
 
@@ -211,9 +213,13 @@ def get_boutiques_output(name, interface, tool_inputs, verbose=False):
     output[
         'optional'] = True  # no real way to determine if an output is always produced, regardless of the input values.
 
+    output['description'] = get_description_from_spec(outputs, name, spec)
+
     # Path template creation.
 
     output_value = interface._list_outputs()[name]
+
+    # If output value is defined, use its basename
     if output_value != "" and isinstance(
             output_value,
             str):  # FIXME: this crashes when there are multiple output values.
@@ -233,11 +239,20 @@ def get_boutiques_output(name, interface, tool_inputs, verbose=False):
                 )  # FIXME: this only works if output is written in the current directory
         output['path-template'] = os.path.basename(output_value)
 
+    # If output value is undefined, create a placeholder for the path template
     if not output_value:
         # Look for an input with the same name and use this as the path template
+        found = False
         for input in tool_inputs:
             if input['id'] == name:
                 output['path-template'] = input['value-key']
+                found = True
+                break
+        # If no input with the same name was found, warn the user they should provide it manually
+        if not found:
+            print("WARNING: Could not determine path template for output %s. Please provide one for the "
+                  "descriptor manually." % name)
+            output['path-template'] = "WARNING: No path template provided."
     return output
 
 
@@ -258,15 +273,21 @@ def get_type_from_spec_info(spec_info):
 
 
 def get_type_from_handler_type(handler):
+    '''
+    Gets the input type from the spec handler type.
+    Returns a tuple containing the type and a boolean to specify
+    if the type is an integer.
+    '''
     handler_type = type(handler).__name__
+    print("TYPE", handler_type)
     if handler_type == "File" or handler_type == "Directory":
-        return "File"
+        return "File", False
     elif handler_type == "Int" or handler_type == "Float":
-        return "Number"
+        return "Number", handler_type == "Int"
     elif handler_type == "Bool":
-        return "Flag"
+        return "Flag", False
     else:
-        return "String"
+        return "String", False
 
 def is_list(spec_info):
     '''
@@ -336,3 +357,20 @@ def must_generate_value(name, type, ignored_template_inputs, spec_info, spec,
     if not ignored_template_inputs:
         return True
     return not (name in ignored_template_inputs)
+
+
+def get_description_from_spec(object, name, spec):
+    '''
+    Generates a description based on the input or output spec.
+    '''
+    if not spec.desc:
+        spec.desc = "No description provided."
+    spec_info = spec.full_info(object, name, None)
+
+    boutiques_description = (spec_info.capitalize(
+    ) + ". " + spec.desc.capitalize()).replace("\n", '')
+
+    if not boutiques_description.endswith('.'):
+        boutiques_description += '.'
+
+    return boutiques_description

From ce068151b7dcc0538f302557ac1b3af3cc86c03d Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Thu, 7 Feb 2019 19:50:29 -0500
Subject: [PATCH 05/28] fixed json file formatting, added save parameter, fixed
 command-line-flag to take argstr from input spec, added requires-inputs and
 disables-inputs

---
 nipype/utils/nipype2boutiques.py | 26 +++++++++++++++++++++-----
 1 file changed, 21 insertions(+), 5 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 83148fc10f..251269167b 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -26,7 +26,7 @@
 
 def generate_boutiques_descriptor(
         module, interface_name, ignored_template_inputs, container_image,
-        container_index, container_type, verbose, ignore_template_numbers):
+        container_index, container_type, verbose, ignore_template_numbers, save):
     '''
     Returns a JSON string containing a JSON Boutiques description of a Nipype interface.
     Arguments:
@@ -37,6 +37,7 @@ def generate_boutiques_descriptor(
     * container_image: name of the container image where the tool is installed
     * container_index: optional index where the image is available
     * container_type: type of container image (Docker or Singularity)
+    * save: True if you want to save descriptor to a file
     '''
 
     if not module:
@@ -102,8 +103,11 @@ def generate_boutiques_descriptor(
         del input['tempvalue']
 
     # Save descriptor to a file
-    with open(interface_name + '.json', 'w') as outfile:
-        json.dump(tool_desc, outfile)
+    if save:
+        with open(interface_name + '.json', 'w') as outfile:
+            json.dump(tool_desc, outfile, indent=4, separators=(',', ': '))
+        if verbose:
+            print("-> Descriptor saved to file " + outfile.name)
 
     print("NOTE: Descriptors produced by this script may not entirely conform to the Nipype interface "
           "specs. Please check that the descriptor is correct before using it.")
@@ -142,7 +146,14 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     input['list'] = is_list(spec_info)
     input['value-key'] = "[" + input_name.upper(
     ) + "]"  # assumes that input names are unique
-    input['command-line-flag'] = ("--%s" % input_name + " ").strip()
+
+    # Add the command line flag specified by argstr
+    # If no argstr is provided and input type is Flag, create a flag from the name
+    if spec.argstr and spec.argstr.split("%")[0]:
+        input['command-line-flag'] = spec.argstr.split("%")[0].strip()
+    elif input['type'] == "Flag":
+        input['command-line-flag'] = ("--%s" % input_name + " ").strip()
+
     input['tempvalue'] = None
     input['description'] = get_description_from_spec(inputs, input_name, spec)
     if not (hasattr(spec, "mandatory") and spec.mandatory):
@@ -160,6 +171,12 @@ def get_boutiques_input(inputs, interface, input_name, spec,
         if value_choices is not None:
             input['value-choices'] = value_choices
 
+    if spec.requires is not None:
+        input['requires-inputs'] = spec.requires
+
+    if spec.xor is not None:
+        input['disables-inputs'] = spec.xor
+
     # Create unique, temporary value.
     temp_value = must_generate_value(input_name, input['type'],
                                      ignored_template_inputs, spec_info, spec,
@@ -279,7 +296,6 @@ def get_type_from_handler_type(handler):
     if the type is an integer.
     '''
     handler_type = type(handler).__name__
-    print("TYPE", handler_type)
     if handler_type == "File" or handler_type == "Directory":
         return "File", False
     elif handler_type == "Int" or handler_type == "Float":

From c1cfc80da1b85beafadb825251f840e700b7dbaa Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Thu, 7 Feb 2019 21:52:33 -0500
Subject: [PATCH 06/28] added logic to deal with range and list inputs, added
 try except block to deal with undefined output values

---
 nipype/utils/nipype2boutiques.py | 68 +++++++++++++++++++++-----------
 1 file changed, 46 insertions(+), 22 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 251269167b..f1a4f46017 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -138,12 +138,48 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     input['name'] = input_name.replace('_', ' ').capitalize()
 
     # Figure out the input type from its handler type
-    input_type = get_type_from_handler_type(spec.handler)
-    input['type'] = input_type[0]
-    if input_type[1]:
+    handler_type = type(spec.handler).__name__
+
+    if handler_type == "File" or handler_type == "Directory":
+        input['type'] = "File"
+    elif handler_type == "Int":
+        input['type'] = "Number"
         input['integer'] = True
+    elif handler_type == "Float":
+        input['type'] = "Number"
+    elif handler_type == "Bool":
+        input['type'] = "Flag"
+    else:
+        input['type'] = "String"
+
+    # Deal with range inputs
+    if handler_type == "Range":
+        input['type'] = "Number"
+        if spec.handler.low is not None:
+            input['minimum'] = spec.handler.low
+        if spec.handler.high is not None:
+            input['maximum'] = spec.handler.high
+        if spec.handler.exclude_low is not None:
+            input['exclusive-minimum'] = spec.handler.exclude_low
+        if spec.handler.exclude_high is not None:
+            input['exclusive-maximum'] = spec.handler.exclude_high
+
+    # Deal with list inputs
+    if handler_type == "List":
+        input['list'] = True
+        trait_type = type(spec.handler.item_trait.trait_type).__name__
+        if trait_type == "Int":
+            input['integer'] = True
+            input['type'] = "Number"
+        elif trait_type == "Float":
+            input['type'] = "Number"
+        else:
+            input['type'] = "String"
+        if spec.handler.minlen is not None:
+            input['min-list-entries'] = spec.handler.minlen
+        if spec.handler.maxlen is not None:
+            input['max-list-entries'] = spec.handler.maxlen
 
-    input['list'] = is_list(spec_info)
     input['value-key'] = "[" + input_name.upper(
     ) + "]"  # assumes that input names are unique
 
@@ -234,7 +270,10 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=Fa
 
     # Path template creation.
 
-    output_value = interface._list_outputs()[name]
+    try:
+        output_value = interface._list_outputs()[name]
+    except TypeError:
+        output_value = None
 
     # If output value is defined, use its basename
     if output_value != "" and isinstance(
@@ -273,7 +312,7 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=Fa
     return output
 
 
-# TODO remove this once we know get_type_from_handler_type works well
+# TODO remove this
 def get_type_from_spec_info(spec_info):
     '''
     Returns an input type from the spec info. There must be a better
@@ -289,22 +328,7 @@ def get_type_from_spec_info(spec_info):
     return "String"
 
 
-def get_type_from_handler_type(handler):
-    '''
-    Gets the input type from the spec handler type.
-    Returns a tuple containing the type and a boolean to specify
-    if the type is an integer.
-    '''
-    handler_type = type(handler).__name__
-    if handler_type == "File" or handler_type == "Directory":
-        return "File", False
-    elif handler_type == "Int" or handler_type == "Float":
-        return "Number", handler_type == "Int"
-    elif handler_type == "Bool":
-        return "Flag", False
-    else:
-        return "String", False
-
+# TODO remove this
 def is_list(spec_info):
     '''
     Returns True if the spec info looks like it describes a list

From ee4b935b3b823df1b61254393632d9c3f7ce70c9 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Mon, 11 Feb 2019 17:25:54 -0500
Subject: [PATCH 07/28] added logic to deal with compound traits, added check
 to make sure inputs don't disable themselves, made default output path
 template the output id

---
 nipype/utils/nipype2boutiques.py            | 81 ++++++++++++++-------
 nipype/utils/tests/test_nipype2boutiques.py |  3 +-
 2 files changed, 57 insertions(+), 27 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index f1a4f46017..34b79437fa 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -78,10 +78,17 @@ def generate_boutiques_descriptor(
         input = get_boutiques_input(inputs, interface, name, spec,
                                     ignored_template_inputs, verbose,
                                     ignore_template_numbers)
-        tool_desc['inputs'].append(input)
-        tool_desc['command-line'] += input['value-key'] + " "
-        if verbose:
-            print("-> Adding input " + input['name'])
+        if isinstance(input, list):
+            for i in input:
+                tool_desc['inputs'].append(i)
+                tool_desc['command-line'] += i['value-key'] + " "
+                if verbose:
+                    print("-> Adding input " + i['name'])
+        else:
+            tool_desc['inputs'].append(input)
+            tool_desc['command-line'] += input['value-key'] + " "
+            if verbose:
+                print("-> Adding input " + input['name'])
 
     # Generates tool outputs
     for name, spec in sorted(outputs.traits(transient=None).items()):
@@ -116,7 +123,7 @@ def generate_boutiques_descriptor(
 
 def get_boutiques_input(inputs, interface, input_name, spec,
                         ignored_template_inputs, verbose,
-                        ignore_template_numbers):
+                        ignore_template_numbers, handler=None, input_number=None):
     """
     Returns a dictionary containing the Boutiques input corresponding to a Nipype intput.
 
@@ -134,11 +141,32 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     spec_info = spec.full_info(inputs, input_name, None)
 
     input = {}
-    input['id'] = input_name
+
+    if input_number is not None:
+        input['id'] = input_name + "_" + str(input_number + 1)
+    else:
+        input['id'] = input_name
+
     input['name'] = input_name.replace('_', ' ').capitalize()
 
+    if handler is None:
+        trait_handler = spec.handler
+    else:
+        trait_handler = handler
+
     # Figure out the input type from its handler type
-    handler_type = type(spec.handler).__name__
+    handler_type = type(trait_handler).__name__
+
+    # Deal with compound traits
+    # TODO create a mutually exclusive group for members of compound traits
+    if handler_type == "TraitCompound":
+        input_list = []
+        # Recursively create an input for each trait
+        for i in range(0, len(trait_handler.handlers)):
+            input_list.append(get_boutiques_input(inputs, interface, input_name, spec,
+                                                  ignored_template_inputs, verbose,
+                                                  ignore_template_numbers, trait_handler.handlers[i], i))
+        return input_list
 
     if handler_type == "File" or handler_type == "Directory":
         input['type'] = "File"
@@ -155,19 +183,19 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     # Deal with range inputs
     if handler_type == "Range":
         input['type'] = "Number"
-        if spec.handler.low is not None:
-            input['minimum'] = spec.handler.low
-        if spec.handler.high is not None:
-            input['maximum'] = spec.handler.high
-        if spec.handler.exclude_low is not None:
-            input['exclusive-minimum'] = spec.handler.exclude_low
-        if spec.handler.exclude_high is not None:
-            input['exclusive-maximum'] = spec.handler.exclude_high
+        if trait_handler.low is not None:
+            input['minimum'] = trait_handler.low
+        if trait_handler.high is not None:
+            input['maximum'] = trait_handler.high
+        if trait_handler.exclude_low is not None:
+            input['exclusive-minimum'] = trait_handler.exclude_low
+        if trait_handler.exclude_high is not None:
+            input['exclusive-maximum'] = trait_handler.exclude_high
 
     # Deal with list inputs
     if handler_type == "List":
         input['list'] = True
-        trait_type = type(spec.handler.item_trait.trait_type).__name__
+        trait_type = type(trait_handler.item_trait.trait_type).__name__
         if trait_type == "Int":
             input['integer'] = True
             input['type'] = "Number"
@@ -175,10 +203,10 @@ def get_boutiques_input(inputs, interface, input_name, spec,
             input['type'] = "Number"
         else:
             input['type'] = "String"
-        if spec.handler.minlen is not None:
-            input['min-list-entries'] = spec.handler.minlen
-        if spec.handler.maxlen is not None:
-            input['max-list-entries'] = spec.handler.maxlen
+        if trait_handler.minlen is not None:
+            input['min-list-entries'] = trait_handler.minlen
+        if trait_handler.maxlen is not None:
+            input['max-list-entries'] = trait_handler.maxlen
 
     input['value-key'] = "[" + input_name.upper(
     ) + "]"  # assumes that input names are unique
@@ -200,7 +228,7 @@ def get_boutiques_input(inputs, interface, input_name, spec,
         input['default-value'] = spec.default_value()[1]
 
     try:
-        value_choices = spec.handler.values
+        value_choices = trait_handler.values
     except AttributeError:
         pass
     else:
@@ -211,7 +239,10 @@ def get_boutiques_input(inputs, interface, input_name, spec,
         input['requires-inputs'] = spec.requires
 
     if spec.xor is not None:
-        input['disables-inputs'] = spec.xor
+        input['disables-inputs'] = list(spec.xor)
+        # Make sure input does not disable itself
+        if input['id'] in input['disables-inputs']:
+            input['disables-inputs'].remove(input['id'])
 
     # Create unique, temporary value.
     temp_value = must_generate_value(input_name, input['type'],
@@ -304,11 +335,9 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=Fa
                 output['path-template'] = input['value-key']
                 found = True
                 break
-        # If no input with the same name was found, warn the user they should provide it manually
+        # If no input with the same name was found, use the output ID
         if not found:
-            print("WARNING: Could not determine path template for output %s. Please provide one for the "
-                  "descriptor manually." % name)
-            output['path-template'] = "WARNING: No path template provided."
+            output['path-template'] = output['id']
     return output
 
 
diff --git a/nipype/utils/tests/test_nipype2boutiques.py b/nipype/utils/tests/test_nipype2boutiques.py
index 3aecefda63..ac12c527f7 100644
--- a/nipype/utils/tests/test_nipype2boutiques.py
+++ b/nipype/utils/tests/test_nipype2boutiques.py
@@ -15,4 +15,5 @@ def test_generate():
                                   container_index=None,
                                   container_type=None,
                                   verbose=False,
-                                  ignore_template_numbers=False)
+                                  ignore_template_numbers=False,
+                                  save=False)

From ad36016e581703ea23d79122a5bfb5a7acb6c54c Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Mon, 11 Feb 2019 22:49:52 -0500
Subject: [PATCH 08/28] put compound inputs into mutex group

---
 nipype/utils/nipype2boutiques.py | 44 ++++++++++----------------------
 1 file changed, 13 insertions(+), 31 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 34b79437fa..2e29be8aba 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -78,12 +78,20 @@ def generate_boutiques_descriptor(
         input = get_boutiques_input(inputs, interface, name, spec,
                                     ignored_template_inputs, verbose,
                                     ignore_template_numbers)
+        # Handle compound inputs (inputs that can be of multiple types and are mutually exclusive)
         if isinstance(input, list):
+            mutex_group_members = []
             for i in input:
                 tool_desc['inputs'].append(i)
                 tool_desc['command-line'] += i['value-key'] + " "
+                mutex_group_members.append(i['id'])
                 if verbose:
                     print("-> Adding input " + i['name'])
+            # Put inputs into a mutually exclusive group
+            tool_desc['groups'] = [{'id': input[0]['id'] + "_group",
+                                    'name': input[0]['name'],
+                                    'members': mutex_group_members,
+                                    'mutually-exclusive': True}]
         else:
             tool_desc['inputs'].append(input)
             tool_desc['command-line'] += input['value-key'] + " "
@@ -123,7 +131,8 @@ def generate_boutiques_descriptor(
 
 def get_boutiques_input(inputs, interface, input_name, spec,
                         ignored_template_inputs, verbose,
-                        ignore_template_numbers, handler=None, input_number=None):
+                        ignore_template_numbers, handler=None,
+                        input_number=None):
     """
     Returns a dictionary containing the Boutiques input corresponding to a Nipype intput.
 
@@ -134,6 +143,8 @@ def get_boutiques_input(inputs, interface, input_name, spec,
       * spec: Nipype input spec.
       * ignored_template_inputs: input names for which no temporary value must be generated.
       * ignore_template_numbers: True if numbers must be ignored in output path creations.
+      * handler: used when handling compound inputs, which don't have their own input spec
+      * input_number: used when handling compound inputs to assign each a unique ID
 
     Assumes that:
       * Input names are unique.
@@ -142,7 +153,7 @@ def get_boutiques_input(inputs, interface, input_name, spec,
 
     input = {}
 
-    if input_number is not None:
+    if input_number is not None and input_number != 0:  # No need to append a number to the first of a list of compound inputs
         input['id'] = input_name + "_" + str(input_number + 1)
     else:
         input['id'] = input_name
@@ -158,7 +169,6 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     handler_type = type(trait_handler).__name__
 
     # Deal with compound traits
-    # TODO create a mutually exclusive group for members of compound traits
     if handler_type == "TraitCompound":
         input_list = []
         # Recursively create an input for each trait
@@ -341,34 +351,6 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=Fa
     return output
 
 
-# TODO remove this
-def get_type_from_spec_info(spec_info):
-    '''
-    Returns an input type from the spec info. There must be a better
-    way to get an input type in Nipype than to parse the spec info.
-    '''
-    if ("an existing file name" in spec_info) or (
-            "input volumes" in spec_info):
-        return "File"
-    elif ("an integer" in spec_info or "a float" in spec_info):
-        return "Number"
-    elif "a boolean" in spec_info:
-        return "Boolean"
-    return "String"
-
-
-# TODO remove this
-def is_list(spec_info):
-    '''
-    Returns True if the spec info looks like it describes a list
-    parameter. There must be a better way in Nipype to check if an input
-    is a list.
-    '''
-    if "a list" in spec_info:
-        return True
-    return False
-
-
 def get_unique_value(type, id):
     '''
     Returns a unique value of type 'type', for input with id 'id',

From bb260f8459a3e8cb016c635f8cea9b7c3e20c4af Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Tue, 12 Feb 2019 15:04:58 -0500
Subject: [PATCH 09/28] added method to get all the mutex and all-or-none
 groups from the input specs

---
 nipype/utils/nipype2boutiques.py | 54 ++++++++++++++++++++++++--------
 1 file changed, 41 insertions(+), 13 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 2e29be8aba..1f46b24885 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -64,6 +64,7 @@ def generate_boutiques_descriptor(
         'description'] = interface_name + ", as implemented in Nipype (module: " + module_name + ", interface: " + interface_name + ")."
     tool_desc['inputs'] = []
     tool_desc['output-files'] = []
+    tool_desc['groups'] = []
     tool_desc['tool-version'] = interface.version if interface.version is not None else "No version provided."
     tool_desc['schema-version'] = '0.5'
     if container_image:
@@ -88,16 +89,21 @@ def generate_boutiques_descriptor(
                 if verbose:
                     print("-> Adding input " + i['name'])
             # Put inputs into a mutually exclusive group
-            tool_desc['groups'] = [{'id': input[0]['id'] + "_group",
-                                    'name': input[0]['name'],
-                                    'members': mutex_group_members,
-                                    'mutually-exclusive': True}]
+            tool_desc['groups'].append({'id': input[0]['id'] + "_group",
+                                        'name': input[0]['name'] + " group",
+                                        'members': mutex_group_members,
+                                        'mutually-exclusive': True})
         else:
             tool_desc['inputs'].append(input)
             tool_desc['command-line'] += input['value-key'] + " "
             if verbose:
                 print("-> Adding input " + input['name'])
 
+    # Generates input groups
+    tool_desc['groups'] += get_boutiques_groups(interface.inputs.traits(transient=None).items())
+    if len(tool_desc['groups']) == 0:
+        del tool_desc['groups']
+
     # Generates tool outputs
     for name, spec in sorted(outputs.traits(transient=None).items()):
         output = get_boutiques_output(outputs, name, spec, interface, tool_desc['inputs'],
@@ -245,15 +251,6 @@ def get_boutiques_input(inputs, interface, input_name, spec,
         if value_choices is not None:
             input['value-choices'] = value_choices
 
-    if spec.requires is not None:
-        input['requires-inputs'] = spec.requires
-
-    if spec.xor is not None:
-        input['disables-inputs'] = list(spec.xor)
-        # Make sure input does not disable itself
-        if input['id'] in input['disables-inputs']:
-            input['disables-inputs'].remove(input['id'])
-
     # Create unique, temporary value.
     temp_value = must_generate_value(input_name, input['type'],
                                      ignored_template_inputs, spec_info, spec,
@@ -351,6 +348,37 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=Fa
     return output
 
 
+def get_boutiques_groups(input_traits):
+    desc_groups = []
+    all_or_none_input_sets = []
+    mutex_input_sets = []
+
+    # Get all the groups
+    for name, spec in input_traits:
+        if spec.requires is not None:
+            group_members = set([name] + list(spec.requires))
+            if group_members not in all_or_none_input_sets:
+                all_or_none_input_sets.append(group_members)
+        if spec.xor is not None:
+            group_members = set([name] + list(spec.xor))
+            if group_members not in mutex_input_sets:
+                mutex_input_sets.append(group_members)
+
+    # Create a dictionary for each one
+    for i in range(0, len(all_or_none_input_sets)):
+        desc_groups.append({'id': "all_or_none_group" + ("_" + str(i + 1) if i != 0 else ""),
+                            'name': "All or none group" + (" " + str(i + 1) if i != 0 else ""),
+                            'members': list(all_or_none_input_sets[i]),
+                            'all-or-none': True})
+
+    for i in range(0, len(mutex_input_sets)):
+        desc_groups.append({'id': "mutex_group" + ("_" + str(i + 1) if i != 0 else ""),
+                            'name': "Mutex group" + (" " + str(i + 1) if i != 0 else ""),
+                            'members': list(mutex_input_sets[i]),
+                            'mutually-exclusive': True})
+
+    return desc_groups
+
 def get_unique_value(type, id):
     '''
     Returns a unique value of type 'type', for input with id 'id',

From 1110b4fcf8e3a242661e55478753cd3488c5fb6b Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Mon, 25 Feb 2019 21:44:15 -0500
Subject: [PATCH 10/28] removed input tempvalue stuff and added logic to rerun
 the interface with various different inputs to try and generate as many
 outputs as possible

---
 nipype/utils/nipype2boutiques.py | 178 +++++++++++++++++++------------
 1 file changed, 109 insertions(+), 69 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 1f46b24885..54d43e94ec 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -25,18 +25,19 @@
 
 
 def generate_boutiques_descriptor(
-        module, interface_name, ignored_template_inputs, container_image,
-        container_index, container_type, verbose, ignore_template_numbers, save):
+        module, interface_name, container_image, container_type, container_index=None,
+        ignored_template_inputs=(), ignore_template_numbers=False, verbose=False, save=False):
     '''
     Returns a JSON string containing a JSON Boutiques description of a Nipype interface.
     Arguments:
     * module: module where the Nipype interface is declared.
     * interface_name: name of Nipype interface.
-    * ignored_template_inputs: a list of input names that should be ignored in the generation of output path templates.
-    * ignore_template_numbers: True if numbers must be ignored in output path creations.
     * container_image: name of the container image where the tool is installed
-    * container_index: optional index where the image is available
     * container_type: type of container image (Docker or Singularity)
+    * container_index: optional index where the image is available
+    * ignored_template_inputs: a list of input names that should be ignored in the generation of output path templates.
+    * ignore_template_numbers: True if numbers must be ignored in output path creations.
+    * verbose: print information messages
     * save: True if you want to save descriptor to a file
     '''
 
@@ -105,23 +106,21 @@ def generate_boutiques_descriptor(
         del tool_desc['groups']
 
     # Generates tool outputs
-    for name, spec in sorted(outputs.traits(transient=None).items()):
-        output = get_boutiques_output(outputs, name, spec, interface, tool_desc['inputs'],
-                                      verbose)
-        if output['path-template'] != "":
-            tool_desc['output-files'].append(output)
-            if verbose:
-                print("-> Adding output " + output['name'])
-        elif verbose:
-            print("xx Skipping output " + output['name'] +
-                  " with no path template.")
-    if tool_desc['output-files'] == []:
-        raise Exception("Tool has no output.")
+    generate_tool_outputs(outputs, interface, tool_desc, verbose, True)
 
-    # Removes all temporary values from inputs (otherwise they will
-    # appear in the JSON output)
-    for input in tool_desc['inputs']:
-        del input['tempvalue']
+    # Generate outputs with various different inputs to try to generate
+    # as many output values as possible
+    custom_inputs = generate_custom_inputs(tool_desc['inputs'])
+
+    for input_dict in custom_inputs:
+        interface = getattr(module, interface_name)(**input_dict)
+        outputs = interface.output_spec()
+        generate_tool_outputs(outputs, interface, tool_desc, verbose, False)
+
+    # Fill in all missing output paths
+    for output in tool_desc['output-files']:
+        if output['path-template'] == "":
+            fill_in_missing_output_path(output, output['name'], tool_desc['inputs'])
 
     # Save descriptor to a file
     if save:
@@ -135,6 +134,26 @@ def generate_boutiques_descriptor(
     return json.dumps(tool_desc, indent=4, separators=(',', ': '))
 
 
+def generate_tool_outputs(outputs, interface, tool_desc, verbose, first_run):
+    for name, spec in sorted(outputs.traits(transient=None).items()):
+        output = get_boutiques_output(outputs, name, spec, interface, tool_desc['inputs'],
+                                      verbose)
+        # If this is the first time we are generating outputs, add the full output to the descriptor.
+        # Otherwise, find the existing output and update its path template if it's still undefined.
+        if first_run:
+            tool_desc['output-files'].append(output)
+        else:
+            for existing_output in tool_desc['output-files']:
+                if output['id'] == existing_output['id'] and existing_output['path-template'] == "":
+                    existing_output['path-template'] = output['path-template']
+                    break
+        if verbose:
+            print("-> Adding output " + output['name'])
+
+    if len(tool_desc['output-files']) == 0:
+        raise Exception("Tool has no output.")
+
+
 def get_boutiques_input(inputs, interface, input_name, spec,
                         ignored_template_inputs, verbose,
                         ignore_template_numbers, handler=None,
@@ -155,7 +174,6 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     Assumes that:
       * Input names are unique.
     """
-    spec_info = spec.full_info(inputs, input_name, None)
 
     input = {}
 
@@ -234,7 +252,6 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     elif input['type'] == "Flag":
         input['command-line-flag'] = ("--%s" % input_name + " ").strip()
 
-    input['tempvalue'] = None
     input['description'] = get_description_from_spec(inputs, input_name, spec)
     if not (hasattr(spec, "mandatory") and spec.mandatory):
         input['optional'] = True
@@ -251,20 +268,7 @@ def get_boutiques_input(inputs, interface, input_name, spec,
         if value_choices is not None:
             input['value-choices'] = value_choices
 
-    # Create unique, temporary value.
-    temp_value = must_generate_value(input_name, input['type'],
-                                     ignored_template_inputs, spec_info, spec,
-                                     ignore_template_numbers)
-    if temp_value:
-        tempvalue = get_unique_value(input['type'], input_name)
-        setattr(interface.inputs, input_name, tempvalue)
-        input['tempvalue'] = tempvalue
-        if verbose:
-            print("oo Path-template creation using " + input['id'] + "=" +
-                  str(tempvalue))
-
-    # Now that temp values have been generated, set Boolean types to
-    # Flag (there is no Boolean type in Boutiques)
+    # Set Boolean types to Flag (there is no Boolean type in Boutiques)
     if input['type'] == "Boolean":
         input['type'] = "Flag"
 
@@ -313,38 +317,13 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=Fa
     except TypeError:
         output_value = None
 
-    # If output value is defined, use its basename
-    if output_value != "" and isinstance(
-            output_value,
-            str):  # FIXME: this crashes when there are multiple output values.
-        # Go find from which input value it was built
-        for input in tool_inputs:
-            if not input['tempvalue']:
-                continue
-            input_value = input['tempvalue']
-            if input['type'] == "File":
-                # Take the base name
-                input_value = os.path.splitext(
-                    os.path.basename(input_value))[0]
-            if str(input_value) in output_value:
-                output_value = os.path.basename(
-                    output_value.replace(input_value,
-                                         input['value-key'])
-                )  # FIXME: this only works if output is written in the current directory
-        output['path-template'] = os.path.basename(output_value)
-
-    # If output value is undefined, create a placeholder for the path template
-    if not output_value:
-        # Look for an input with the same name and use this as the path template
-        found = False
-        for input in tool_inputs:
-            if input['id'] == name:
-                output['path-template'] = input['value-key']
-                found = True
-                break
-        # If no input with the same name was found, use the output ID
-        if not found:
-            output['path-template'] = output['id']
+    # If an output value is defined, use its relative path
+    # Otherwise, put blank string and try to fill it on another iteration
+    if output_value:
+        output['path-template'] = os.path.relpath(output_value)
+    else:
+        output['path-template'] = ""
+
     return output
 
 
@@ -379,6 +358,7 @@ def get_boutiques_groups(input_traits):
 
     return desc_groups
 
+
 def get_unique_value(type, id):
     '''
     Returns a unique value of type 'type', for input with id 'id',
@@ -453,3 +433,63 @@ def get_description_from_spec(object, name, spec):
         boutiques_description += '.'
 
     return boutiques_description
+
+
+def fill_in_missing_output_path(output, output_name, tool_inputs):
+    '''
+    Creates a path template for outputs that are missing one
+    This is needed for the descriptor to be valid (path template is required)
+    '''
+    # Look for an input with the same name as the output and use its value key
+    found = False
+    for input in tool_inputs:
+        if input['name'] == output_name:
+            output['path-template'] = input['value-key']
+            found = True
+            break
+    # If no input with the same name was found, use the output ID
+    if not found:
+        output['path-template'] = output['id']
+    return output
+
+
+
+def generate_custom_inputs(desc_inputs):
+    '''
+    Generates a bunch of custom input dictionaries in order to generate as many outputs as possible
+    (to get their path templates)
+    Limitations:
+       -Does not support String inputs since some interfaces require specific strings
+       -Does not support File inputs since the file has to actually exist or the interface will fail
+       -Does not support list inputs yet
+    '''
+    custom_input_dicts = []
+    for desc_input in desc_inputs:
+        if desc_input.get('list'):  # TODO support list inputs
+            continue
+        if desc_input['type'] == 'Flag':
+            custom_input_dicts.append({desc_input['id']: True})
+        elif desc_input['type'] == 'Number':
+            custom_input_dicts.append({desc_input['id']: generate_random_number_input(desc_input)})
+        elif desc_input.get('value-choices'):
+            for value in desc_input['value-choices']:
+                custom_input_dicts.append({desc_input['id']: value})
+    return custom_input_dicts
+
+
+def generate_random_number_input(desc_input):
+    '''
+    Generates a random number input based on the input spec
+    '''
+    if not desc_input.get('minimum') and not desc_input.get('maximum'):
+        return 1
+
+    if desc_input.get('integer'):
+        offset = 1
+    else:
+        offset = 0.1
+
+    if desc_input.get('minimum'):
+        return desc_input['minimum'] if desc_input.get('exclusive-minimum') else desc_input['minimum'] + offset
+    if desc_input.get('maximum'):
+        return desc_input['maximum'] if desc_input.get('exclusive-maximum') else desc_input['maximum'] - offset

From 8e20d2d142452c48e0bb6c9f876e2d29b9746e5f Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Mon, 25 Feb 2019 23:42:01 -0500
Subject: [PATCH 11/28] added logic to handle multioutputs and inputs where
 value choices are numbers, some other minor fixes

---
 nipype/utils/nipype2boutiques.py | 53 ++++++++++++++++++++++++++------
 1 file changed, 43 insertions(+), 10 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 54d43e94ec..852887052f 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -20,6 +20,8 @@
 import sys
 import tempfile
 import simplejson as json
+import copy
+import six
 
 from ..scripts.instance import import_module
 
@@ -83,9 +85,9 @@ def generate_boutiques_descriptor(
         # Handle compound inputs (inputs that can be of multiple types and are mutually exclusive)
         if isinstance(input, list):
             mutex_group_members = []
+            tool_desc['command-line'] += input[0]['value-key'] + " "
             for i in input:
                 tool_desc['inputs'].append(i)
-                tool_desc['command-line'] += i['value-key'] + " "
                 mutex_group_members.append(i['id'])
                 if verbose:
                     print("-> Adding input " + i['name'])
@@ -100,6 +102,9 @@ def generate_boutiques_descriptor(
             if verbose:
                 print("-> Adding input " + input['name'])
 
+    # Remove the extra space at the end of the command line
+    tool_desc['command-line'] = tool_desc['command-line'].strip()
+
     # Generates input groups
     tool_desc['groups'] += get_boutiques_groups(interface.inputs.traits(transient=None).items())
     if len(tool_desc['groups']) == 0:
@@ -141,14 +146,20 @@ def generate_tool_outputs(outputs, interface, tool_desc, verbose, first_run):
         # If this is the first time we are generating outputs, add the full output to the descriptor.
         # Otherwise, find the existing output and update its path template if it's still undefined.
         if first_run:
-            tool_desc['output-files'].append(output)
+            if isinstance(output, list):
+                tool_desc['output-files'].extend(output)
+                if verbose:
+                    print("-> Adding output " + output[0]['name'])
+            else:
+                tool_desc['output-files'].append(output)
+                if verbose:
+                    print("-> Adding output " + output['name'])
         else:
             for existing_output in tool_desc['output-files']:
-                if output['id'] == existing_output['id'] and existing_output['path-template'] == "":
+                if not isinstance(output, list) and output['id'] == existing_output['id'] \
+                        and existing_output['path-template'] == "":
                     existing_output['path-template'] = output['path-template']
                     break
-        if verbose:
-            print("-> Adding output " + output['name'])
 
     if len(tool_desc['output-files']) == 0:
         raise Exception("Tool has no output.")
@@ -197,9 +208,11 @@ def get_boutiques_input(inputs, interface, input_name, spec,
         input_list = []
         # Recursively create an input for each trait
         for i in range(0, len(trait_handler.handlers)):
-            input_list.append(get_boutiques_input(inputs, interface, input_name, spec,
-                                                  ignored_template_inputs, verbose,
-                                                  ignore_template_numbers, trait_handler.handlers[i], i))
+            inp = get_boutiques_input(inputs, interface, input_name, spec,
+                                      ignored_template_inputs, verbose,
+                                      ignore_template_numbers, trait_handler.handlers[i], i)
+            inp['optional'] = True
+            input_list.append(inp)
         return input_list
 
     if handler_type == "File" or handler_type == "Directory":
@@ -227,6 +240,7 @@ def get_boutiques_input(inputs, interface, input_name, spec,
             input['exclusive-maximum'] = trait_handler.exclude_high
 
     # Deal with list inputs
+    # TODO handle lists of lists (e.g. FSL ProbTrackX seed input)
     if handler_type == "List":
         input['list'] = True
         trait_type = type(trait_handler.item_trait.trait_type).__name__
@@ -235,11 +249,13 @@ def get_boutiques_input(inputs, interface, input_name, spec,
             input['type'] = "Number"
         elif trait_type == "Float":
             input['type'] = "Number"
+        elif trait_type == "File":
+            input['type'] = "File"
         else:
             input['type'] = "String"
-        if trait_handler.minlen is not None:
+        if trait_handler.minlen != 0:
             input['min-list-entries'] = trait_handler.minlen
-        if trait_handler.maxlen is not None:
+        if trait_handler.maxlen != six.MAXSIZE:
             input['max-list-entries'] = trait_handler.maxlen
 
     input['value-key'] = "[" + input_name.upper(
@@ -266,6 +282,11 @@ def get_boutiques_input(inputs, interface, input_name, spec,
         pass
     else:
         if value_choices is not None:
+            if all(isinstance(n, int) for n in value_choices):
+                input['type'] = "Number"
+                input['integer'] = True
+            elif all(isinstance(n, float) for n in value_choices):
+                input['type'] = "Number"
             input['value-choices'] = value_choices
 
     # Set Boolean types to Flag (there is no Boolean type in Boutiques)
@@ -316,6 +337,18 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=Fa
         output_value = interface._list_outputs()[name]
     except TypeError:
         output_value = None
+    except AttributeError:
+        output_value = None
+
+    # Handle multi-outputs
+    if isinstance(output_value, list):
+        output_list = []
+        for i in range(0, len(output_value)):
+            output_copy = copy.deepcopy(output)
+            output_copy['path-template'] = os.path.relpath(output_value[i])
+            output_copy['id'] += ("_" + str(i+1)) if i > 0 else ""
+            output_list.append(output_copy)
+        return output_list
 
     # If an output value is defined, use its relative path
     # Otherwise, put blank string and try to fill it on another iteration

From 61c836fcdf168afb8556244b4c36753213967153 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Tue, 26 Feb 2019 14:22:46 -0500
Subject: [PATCH 12/28] fixed multioutput, added handling of multiinput, added
 option to supply custom path for saved file

---
 nipype/utils/nipype2boutiques.py | 44 ++++++++++++++++++--------------
 1 file changed, 25 insertions(+), 19 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 852887052f..41492640bb 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -28,7 +28,7 @@
 
 def generate_boutiques_descriptor(
         module, interface_name, container_image, container_type, container_index=None,
-        ignored_template_inputs=(), ignore_template_numbers=False, verbose=False, save=False):
+        ignored_template_inputs=(), ignore_template_numbers=False, verbose=False, save=False, save_path=None):
     '''
     Returns a JSON string containing a JSON Boutiques description of a Nipype interface.
     Arguments:
@@ -41,6 +41,7 @@ def generate_boutiques_descriptor(
     * ignore_template_numbers: True if numbers must be ignored in output path creations.
     * verbose: print information messages
     * save: True if you want to save descriptor to a file
+    * save_path: file path for the saved descriptor (defaults to name of the interface in current directory)
     '''
 
     if not module:
@@ -129,7 +130,8 @@ def generate_boutiques_descriptor(
 
     # Save descriptor to a file
     if save:
-        with open(interface_name + '.json', 'w') as outfile:
+        path = save_path if save_path is not None else os.path.join(os.getcwd(), interface_name + '.json')
+        with open(path, 'w') as outfile:
             json.dump(tool_desc, outfile, indent=4, separators=(',', ': '))
         if verbose:
             print("-> Descriptor saved to file " + outfile.name)
@@ -146,18 +148,12 @@ def generate_tool_outputs(outputs, interface, tool_desc, verbose, first_run):
         # If this is the first time we are generating outputs, add the full output to the descriptor.
         # Otherwise, find the existing output and update its path template if it's still undefined.
         if first_run:
-            if isinstance(output, list):
-                tool_desc['output-files'].extend(output)
-                if verbose:
-                    print("-> Adding output " + output[0]['name'])
-            else:
-                tool_desc['output-files'].append(output)
-                if verbose:
-                    print("-> Adding output " + output['name'])
+            tool_desc['output-files'].append(output)
+            if verbose:
+                print("-> Adding output " + output['name'])
         else:
             for existing_output in tool_desc['output-files']:
-                if not isinstance(output, list) and output['id'] == existing_output['id'] \
-                        and existing_output['path-template'] == "":
+                if output['id'] == existing_output['id'] and existing_output['path-template'] == "":
                     existing_output['path-template'] = output['path-template']
                     break
 
@@ -258,6 +254,11 @@ def get_boutiques_input(inputs, interface, input_name, spec,
         if trait_handler.maxlen != six.MAXSIZE:
             input['max-list-entries'] = trait_handler.maxlen
 
+    # Deal with multi-input
+    if handler_type == "InputMultiObject":
+        input['type'] = "File"
+        input['list'] = True
+
     input['value-key'] = "[" + input_name.upper(
     ) + "]"  # assumes that input names are unique
 
@@ -342,13 +343,18 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=Fa
 
     # Handle multi-outputs
     if isinstance(output_value, list):
-        output_list = []
-        for i in range(0, len(output_value)):
-            output_copy = copy.deepcopy(output)
-            output_copy['path-template'] = os.path.relpath(output_value[i])
-            output_copy['id'] += ("_" + str(i+1)) if i > 0 else ""
-            output_list.append(output_copy)
-        return output_list
+        output['list'] = True
+        # Check if all extensions are the same
+        extensions = []
+        for val in output_value:
+            extensions.append(os.path.splitext(val)[1])
+        # If extensions all the same, set path template as wildcard + extension
+        # Otherwise just use a wildcard
+        if len(set(extensions)) == 1:
+            output['path-template'] = "*" + extensions[0]
+        else:
+            output['path-template'] = "*"
+        return output
 
     # If an output value is defined, use its relative path
     # Otherwise, put blank string and try to fill it on another iteration

From f4c8867f88b0895c1531e961c6b693981d6ebcf7 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Tue, 26 Feb 2019 15:56:35 -0500
Subject: [PATCH 13/28] fixed number input min and max, removed numbers from
 custom inputs (caused too many failures)

---
 nipype/utils/nipype2boutiques.py | 26 +++++++++-----------------
 1 file changed, 9 insertions(+), 17 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 41492640bb..8ff2d11880 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -226,14 +226,14 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     # Deal with range inputs
     if handler_type == "Range":
         input['type'] = "Number"
-        if trait_handler.low is not None:
-            input['minimum'] = trait_handler.low
-        if trait_handler.high is not None:
-            input['maximum'] = trait_handler.high
-        if trait_handler.exclude_low is not None:
-            input['exclusive-minimum'] = trait_handler.exclude_low
-        if trait_handler.exclude_high is not None:
-            input['exclusive-maximum'] = trait_handler.exclude_high
+        if trait_handler._low is not None:
+            input['minimum'] = trait_handler._low
+        if trait_handler._high is not None:
+            input['maximum'] = trait_handler._high
+        if trait_handler._exclude_low:
+            input['exclusive-minimum'] = True
+        if trait_handler._exclude_high:
+            input['exclusive-maximum'] = True
 
     # Deal with list inputs
     # TODO handle lists of lists (e.g. FSL ProbTrackX seed input)
@@ -492,24 +492,16 @@ def fill_in_missing_output_path(output, output_name, tool_inputs):
     return output
 
 
-
 def generate_custom_inputs(desc_inputs):
     '''
     Generates a bunch of custom input dictionaries in order to generate as many outputs as possible
     (to get their path templates)
-    Limitations:
-       -Does not support String inputs since some interfaces require specific strings
-       -Does not support File inputs since the file has to actually exist or the interface will fail
-       -Does not support list inputs yet
+    Currently only works with flag inputs and inputs with defined value choices.
     '''
     custom_input_dicts = []
     for desc_input in desc_inputs:
-        if desc_input.get('list'):  # TODO support list inputs
-            continue
         if desc_input['type'] == 'Flag':
             custom_input_dicts.append({desc_input['id']: True})
-        elif desc_input['type'] == 'Number':
-            custom_input_dicts.append({desc_input['id']: generate_random_number_input(desc_input)})
         elif desc_input.get('value-choices'):
             for value in desc_input['value-choices']:
                 custom_input_dicts.append({desc_input['id']: value})

From 6961f02bcb1ba0e85c7de6a85ba34d74755f3dc1 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Tue, 26 Feb 2019 16:39:03 -0500
Subject: [PATCH 14/28] removed unused things, updated comments

---
 nipype/utils/nipype2boutiques.py            | 112 ++------------------
 nipype/utils/tests/test_nipype2boutiques.py |   2 -
 2 files changed, 11 insertions(+), 103 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 8ff2d11880..ff389fdb52 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -7,20 +7,12 @@
 # Boutiques tools can be imported in CBRAIN (https://github.com/aces/cbrain) among other platforms.
 #
 # Limitations:
-#   * List outputs are not supported.
-#   * Default values are not extracted from the documentation of the Nipype interface.
-#   * The following input types must be ignored for the output path template creation (see option -t):
-#     ** String restrictions, i.e. String inputs that accept only a restricted set of values.
-#     ** mutually exclusive inputs.
-#   * Path-templates are wrong when output files are not created in the execution directory (e.g. when a sub-directory is created).
-#   * Optional outputs, i.e. outputs that not always produced, may not be detected.
+#   * Optional outputs, i.e. outputs that not always produced, may not be detected. They will, however, still be listed
+#     with a placeholder for the path template (either a value key or the output ID) that should be verified and corrected.
 
 import os
-import argparse
 import sys
-import tempfile
 import simplejson as json
-import copy
 import six
 
 from ..scripts.instance import import_module
@@ -28,7 +20,7 @@
 
 def generate_boutiques_descriptor(
         module, interface_name, container_image, container_type, container_index=None,
-        ignored_template_inputs=(), ignore_template_numbers=False, verbose=False, save=False, save_path=None):
+        verbose=False, save=False, save_path=None):
     '''
     Returns a JSON string containing a JSON Boutiques description of a Nipype interface.
     Arguments:
@@ -37,8 +29,6 @@ def generate_boutiques_descriptor(
     * container_image: name of the container image where the tool is installed
     * container_type: type of container image (Docker or Singularity)
     * container_index: optional index where the image is available
-    * ignored_template_inputs: a list of input names that should be ignored in the generation of output path templates.
-    * ignore_template_numbers: True if numbers must be ignored in output path creations.
     * verbose: print information messages
     * save: True if you want to save descriptor to a file
     * save_path: file path for the saved descriptor (defaults to name of the interface in current directory)
@@ -80,9 +70,7 @@ def generate_boutiques_descriptor(
 
     # Generates tool inputs
     for name, spec in sorted(interface.inputs.traits(transient=None).items()):
-        input = get_boutiques_input(inputs, interface, name, spec,
-                                    ignored_template_inputs, verbose,
-                                    ignore_template_numbers)
+        input = get_boutiques_input(inputs, interface, name, spec, verbose)
         # Handle compound inputs (inputs that can be of multiple types and are mutually exclusive)
         if isinstance(input, list):
             mutex_group_members = []
@@ -162,9 +150,7 @@ def generate_tool_outputs(outputs, interface, tool_desc, verbose, first_run):
 
 
 def get_boutiques_input(inputs, interface, input_name, spec,
-                        ignored_template_inputs, verbose,
-                        ignore_template_numbers, handler=None,
-                        input_number=None):
+                        verbose, handler=None, input_number=None):
     """
     Returns a dictionary containing the Boutiques input corresponding to a Nipype intput.
 
@@ -173,8 +159,7 @@ def get_boutiques_input(inputs, interface, input_name, spec,
       * interface: Nipype interface.
       * input_name: name of the Nipype input.
       * spec: Nipype input spec.
-      * ignored_template_inputs: input names for which no temporary value must be generated.
-      * ignore_template_numbers: True if numbers must be ignored in output path creations.
+      * verbose: print information messages.
       * handler: used when handling compound inputs, which don't have their own input spec
       * input_number: used when handling compound inputs to assign each a unique ID
 
@@ -205,8 +190,7 @@ def get_boutiques_input(inputs, interface, input_name, spec,
         # Recursively create an input for each trait
         for i in range(0, len(trait_handler.handlers)):
             inp = get_boutiques_input(inputs, interface, input_name, spec,
-                                      ignored_template_inputs, verbose,
-                                      ignore_template_numbers, trait_handler.handlers[i], i)
+                                      verbose, trait_handler.handlers[i], i)
             inp['optional'] = True
             input_list.append(inp)
         return input_list
@@ -297,7 +281,7 @@ def get_boutiques_input(inputs, interface, input_name, spec,
     return input
 
 
-def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=False):
+def get_boutiques_output(outputs, name, spec, interface, tool_inputs):
     """
     Returns a dictionary containing the Boutiques output corresponding to a Nipype output.
 
@@ -367,6 +351,9 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs, verbose=Fa
 
 
 def get_boutiques_groups(input_traits):
+    """
+    Returns a list of dictionaries containing Boutiques groups for the mutually exclusive and all-or-none Nipype inputs.
+    """
     desc_groups = []
     all_or_none_input_sets = []
     mutex_input_sets = []
@@ -398,65 +385,6 @@ def get_boutiques_groups(input_traits):
     return desc_groups
 
 
-def get_unique_value(type, id):
-    '''
-    Returns a unique value of type 'type', for input with id 'id',
-    assuming id is unique.
-    '''
-    return {
-        "File": os.path.abspath(create_tempfile()),
-        "Boolean": True,
-        "Number": abs(hash(id)),  # abs in case input param must be positive...
-        "String": id
-    }[type]
-
-
-def create_tempfile():
-    '''
-    Creates a temp file and returns its name.
-    '''
-    fileTemp = tempfile.NamedTemporaryFile(delete=False)
-    fileTemp.write(b"hello")
-    fileTemp.close()
-    return fileTemp.name
-
-
-def must_generate_value(name, type, ignored_template_inputs, spec_info, spec,
-                        ignore_template_numbers):
-    '''
-    Return True if a temporary value must be generated for this input.
-    Arguments:
-    * name: input name.
-    * type: input_type.
-    * ignored_template_inputs: a list of inputs names for which no value must be generated.
-    * spec_info: spec info of the Nipype input
-    * ignore_template_numbers: True if numbers must be ignored.
-    '''
-    # Return false when type is number and numbers must be ignored.
-    if ignore_template_numbers and type == "Number":
-        return False
-    # Only generate value for the first element of mutually exclusive inputs.
-    if spec.xor and spec.xor[0] != name:
-        return False
-    # Directory types are not supported
-    if "an existing directory name" in spec_info:
-        return False
-    # Don't know how to generate a list.
-    if "a list" in spec_info or "a tuple" in spec_info:
-        return False
-    # Don't know how to generate a dictionary.
-    if "a dictionary" in spec_info:
-        return False
-    # Best guess to detect string restrictions...
-    if "' or '" in spec_info:
-        return False
-    if spec.default or spec.default_value():
-        return False
-    if not ignored_template_inputs:
-        return True
-    return not (name in ignored_template_inputs)
-
-
 def get_description_from_spec(object, name, spec):
     '''
     Generates a description based on the input or output spec.
@@ -506,21 +434,3 @@ def generate_custom_inputs(desc_inputs):
             for value in desc_input['value-choices']:
                 custom_input_dicts.append({desc_input['id']: value})
     return custom_input_dicts
-
-
-def generate_random_number_input(desc_input):
-    '''
-    Generates a random number input based on the input spec
-    '''
-    if not desc_input.get('minimum') and not desc_input.get('maximum'):
-        return 1
-
-    if desc_input.get('integer'):
-        offset = 1
-    else:
-        offset = 0.1
-
-    if desc_input.get('minimum'):
-        return desc_input['minimum'] if desc_input.get('exclusive-minimum') else desc_input['minimum'] + offset
-    if desc_input.get('maximum'):
-        return desc_input['maximum'] if desc_input.get('exclusive-maximum') else desc_input['maximum'] - offset
diff --git a/nipype/utils/tests/test_nipype2boutiques.py b/nipype/utils/tests/test_nipype2boutiques.py
index ac12c527f7..926de0f2cd 100644
--- a/nipype/utils/tests/test_nipype2boutiques.py
+++ b/nipype/utils/tests/test_nipype2boutiques.py
@@ -10,10 +10,8 @@
 def test_generate():
     generate_boutiques_descriptor(module='nipype.interfaces.ants.registration',
                                   interface_name='ANTS',
-                                  ignored_template_inputs=(),
                                   container_image=None,
                                   container_index=None,
                                   container_type=None,
                                   verbose=False,
-                                  ignore_template_numbers=False,
                                   save=False)

From f67d04b4b1c45728ca1961f8c11b859c35f5a852 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Wed, 27 Feb 2019 19:20:43 -0500
Subject: [PATCH 15/28] fixed small error

---
 nipype/utils/nipype2boutiques.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index ff389fdb52..aba64c4414 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -131,8 +131,7 @@ def generate_boutiques_descriptor(
 
 def generate_tool_outputs(outputs, interface, tool_desc, verbose, first_run):
     for name, spec in sorted(outputs.traits(transient=None).items()):
-        output = get_boutiques_output(outputs, name, spec, interface, tool_desc['inputs'],
-                                      verbose)
+        output = get_boutiques_output(outputs, name, spec, interface, tool_desc['inputs'])
         # If this is the first time we are generating outputs, add the full output to the descriptor.
         # Otherwise, find the existing output and update its path template if it's still undefined.
         if first_run:

From 2bf03cf1d6287984da2606cadde30d12e7408102 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Tue, 12 Mar 2019 16:20:32 -0400
Subject: [PATCH 16/28] added author and ignored inputs parameters, removed
 nipype from command line, added logic to deal with inputs containing
 name_source and name_template metadata

---
 nipype/utils/nipype2boutiques.py | 53 +++++++++++++++++++++++++-------
 1 file changed, 42 insertions(+), 11 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index aba64c4414..0472673469 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -20,7 +20,7 @@
 
 def generate_boutiques_descriptor(
         module, interface_name, container_image, container_type, container_index=None,
-        verbose=False, save=False, save_path=None):
+        verbose=False, save=False, save_path=None, author=None, ignore_inputs=None):
     '''
     Returns a JSON string containing a JSON Boutiques description of a Nipype interface.
     Arguments:
@@ -32,6 +32,8 @@ def generate_boutiques_descriptor(
     * verbose: print information messages
     * save: True if you want to save descriptor to a file
     * save_path: file path for the saved descriptor (defaults to name of the interface in current directory)
+    * author: author of the tool (required for publishing)
+    * ignore_inputs: list of interface inputs to not include in the descriptor
     '''
 
     if not module:
@@ -53,7 +55,10 @@ def generate_boutiques_descriptor(
     tool_desc = {}
     tool_desc['name'] = interface_name
     tool_desc[
-        'command-line'] = "nipype_cmd " + module_name + " " + interface_name + " "
+        'command-line'] = interface_name + " "
+    tool_desc['author'] = "Nipype (interface)"
+    if author is not None:
+        tool_desc['author'] = tool_desc['author'] + ", " + author + " (tool)"
     tool_desc[
         'description'] = interface_name + ", as implemented in Nipype (module: " + module_name + ", interface: " + interface_name + ")."
     tool_desc['inputs'] = []
@@ -70,8 +75,10 @@ def generate_boutiques_descriptor(
 
     # Generates tool inputs
     for name, spec in sorted(interface.inputs.traits(transient=None).items()):
-        input = get_boutiques_input(inputs, interface, name, spec, verbose)
+        input = get_boutiques_input(inputs, interface, name, spec, verbose, ignore_inputs=ignore_inputs)
         # Handle compound inputs (inputs that can be of multiple types and are mutually exclusive)
+        if input is None:
+            continue
         if isinstance(input, list):
             mutex_group_members = []
             tool_desc['command-line'] += input[0]['value-key'] + " "
@@ -91,9 +98,6 @@ def generate_boutiques_descriptor(
             if verbose:
                 print("-> Adding input " + input['name'])
 
-    # Remove the extra space at the end of the command line
-    tool_desc['command-line'] = tool_desc['command-line'].strip()
-
     # Generates input groups
     tool_desc['groups'] += get_boutiques_groups(interface.inputs.traits(transient=None).items())
     if len(tool_desc['groups']) == 0:
@@ -116,6 +120,9 @@ def generate_boutiques_descriptor(
         if output['path-template'] == "":
             fill_in_missing_output_path(output, output['name'], tool_desc['inputs'])
 
+    # Remove the extra space at the end of the command line
+    tool_desc['command-line'] = tool_desc['command-line'].strip()
+
     # Save descriptor to a file
     if save:
         path = save_path if save_path is not None else os.path.join(os.getcwd(), interface_name + '.json')
@@ -136,6 +143,8 @@ def generate_tool_outputs(outputs, interface, tool_desc, verbose, first_run):
         # Otherwise, find the existing output and update its path template if it's still undefined.
         if first_run:
             tool_desc['output-files'].append(output)
+            if output.get('value-key'):
+                tool_desc['command-line'] += output['value-key'] + " "
             if verbose:
                 print("-> Adding output " + output['name'])
         else:
@@ -143,13 +152,15 @@ def generate_tool_outputs(outputs, interface, tool_desc, verbose, first_run):
                 if output['id'] == existing_output['id'] and existing_output['path-template'] == "":
                     existing_output['path-template'] = output['path-template']
                     break
+            if output.get('value-key') and output['value-key'] not in tool_desc['command-line']:
+                tool_desc['command-line'] += output['value-key'] + " "
 
     if len(tool_desc['output-files']) == 0:
         raise Exception("Tool has no output.")
 
 
-def get_boutiques_input(inputs, interface, input_name, spec,
-                        verbose, handler=None, input_number=None):
+def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=None,
+                        input_number=None, ignore_inputs=None):
     """
     Returns a dictionary containing the Boutiques input corresponding to a Nipype intput.
 
@@ -161,11 +172,17 @@ def get_boutiques_input(inputs, interface, input_name, spec,
       * verbose: print information messages.
       * handler: used when handling compound inputs, which don't have their own input spec
       * input_number: used when handling compound inputs to assign each a unique ID
+      * ignore_inputs: list of interface inputs to not include in the descriptor
 
     Assumes that:
       * Input names are unique.
     """
 
+    # If spec has a name source, means it's an output, so skip it here.
+    # Also skip any ignored inputs
+    if spec.name_source or ignore_inputs is not None and input_name in ignore_inputs:
+        return None
+
     input = {}
 
     if input_number is not None and input_number != 0:  # No need to append a number to the first of a list of compound inputs
@@ -339,12 +356,26 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs):
             output['path-template'] = "*"
         return output
 
-    # If an output value is defined, use its relative path
-    # Otherwise, put blank string and try to fill it on another iteration
+    # If an output value is defined, use its relative path, if one exists.
+    # If no relative path, look for an input with the same name containing a name source
+    # and name template. Otherwise, put blank string as placeholder and try to fill it on
+    # another iteration.
+    output['path-template'] = ""
+
     if output_value:
         output['path-template'] = os.path.relpath(output_value)
     else:
-        output['path-template'] = ""
+        for inp_name, inp_spec in sorted(interface.inputs.traits(transient=None).items()):
+            if inp_name == name and inp_spec.name_source and inp_spec.name_template:
+                if isinstance(inp_spec.name_source, list):
+                    source = inp_spec.name_source[0]
+                else:
+                    source = inp_spec.name_source
+                output['path-template'] = inp_spec.name_template.replace("%s", "[" + source.upper() + "]")
+                output['value-key'] = "[" + name.upper() + "]"
+                if inp_spec.argstr and inp_spec.argstr.split("%")[0]:
+                    output['command-line-flag'] = inp_spec.argstr.split("%")[0].strip()
+                break
 
     return output
 

From d009a88ac46e8971bf727f1221f18808014f74be Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Tue, 12 Mar 2019 16:57:10 -0400
Subject: [PATCH 17/28] fixed code quality issues

---
 nipype/utils/nipype2boutiques.py | 120 +++++++++++++++----------------
 1 file changed, 60 insertions(+), 60 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 0472673469..e5b91b0ea7 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -75,28 +75,28 @@ def generate_boutiques_descriptor(
 
     # Generates tool inputs
     for name, spec in sorted(interface.inputs.traits(transient=None).items()):
-        input = get_boutiques_input(inputs, interface, name, spec, verbose, ignore_inputs=ignore_inputs)
+        inp = get_boutiques_input(inputs, interface, name, spec, verbose, ignore_inputs=ignore_inputs)
         # Handle compound inputs (inputs that can be of multiple types and are mutually exclusive)
-        if input is None:
+        if inp is None:
             continue
-        if isinstance(input, list):
+        if isinstance(inp, list):
             mutex_group_members = []
-            tool_desc['command-line'] += input[0]['value-key'] + " "
-            for i in input:
+            tool_desc['command-line'] += inp[0]['value-key'] + " "
+            for i in inp:
                 tool_desc['inputs'].append(i)
                 mutex_group_members.append(i['id'])
                 if verbose:
                     print("-> Adding input " + i['name'])
             # Put inputs into a mutually exclusive group
-            tool_desc['groups'].append({'id': input[0]['id'] + "_group",
-                                        'name': input[0]['name'] + " group",
+            tool_desc['groups'].append({'id': inp[0]['id'] + "_group",
+                                        'name': inp[0]['name'] + " group",
                                         'members': mutex_group_members,
                                         'mutually-exclusive': True})
         else:
-            tool_desc['inputs'].append(input)
-            tool_desc['command-line'] += input['value-key'] + " "
+            tool_desc['inputs'].append(inp)
+            tool_desc['command-line'] += inp['value-key'] + " "
             if verbose:
-                print("-> Adding input " + input['name'])
+                print("-> Adding input " + inp['name'])
 
     # Generates input groups
     tool_desc['groups'] += get_boutiques_groups(interface.inputs.traits(transient=None).items())
@@ -183,14 +183,14 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
     if spec.name_source or ignore_inputs is not None and input_name in ignore_inputs:
         return None
 
-    input = {}
+    inp = {}
 
     if input_number is not None and input_number != 0:  # No need to append a number to the first of a list of compound inputs
-        input['id'] = input_name + "_" + str(input_number + 1)
+        inp['id'] = input_name + "_" + str(input_number + 1)
     else:
-        input['id'] = input_name
+        inp['id'] = input_name
 
-    input['name'] = input_name.replace('_', ' ').capitalize()
+    inp['name'] = input_name.replace('_', ' ').capitalize()
 
     if handler is None:
         trait_handler = spec.handler
@@ -212,70 +212,70 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
         return input_list
 
     if handler_type == "File" or handler_type == "Directory":
-        input['type'] = "File"
+        inp['type'] = "File"
     elif handler_type == "Int":
-        input['type'] = "Number"
-        input['integer'] = True
+        inp['type'] = "Number"
+        inp['integer'] = True
     elif handler_type == "Float":
-        input['type'] = "Number"
+        inp['type'] = "Number"
     elif handler_type == "Bool":
-        input['type'] = "Flag"
+        inp['type'] = "Flag"
     else:
-        input['type'] = "String"
+        inp['type'] = "String"
 
     # Deal with range inputs
     if handler_type == "Range":
-        input['type'] = "Number"
+        inp['type'] = "Number"
         if trait_handler._low is not None:
-            input['minimum'] = trait_handler._low
+            inp['minimum'] = trait_handler._low
         if trait_handler._high is not None:
-            input['maximum'] = trait_handler._high
+            inp['maximum'] = trait_handler._high
         if trait_handler._exclude_low:
-            input['exclusive-minimum'] = True
+            inp['exclusive-minimum'] = True
         if trait_handler._exclude_high:
-            input['exclusive-maximum'] = True
+            inp['exclusive-maximum'] = True
 
     # Deal with list inputs
     # TODO handle lists of lists (e.g. FSL ProbTrackX seed input)
     if handler_type == "List":
-        input['list'] = True
+        inp['list'] = True
         trait_type = type(trait_handler.item_trait.trait_type).__name__
         if trait_type == "Int":
-            input['integer'] = True
-            input['type'] = "Number"
+            inp['integer'] = True
+            inp['type'] = "Number"
         elif trait_type == "Float":
-            input['type'] = "Number"
+            inp['type'] = "Number"
         elif trait_type == "File":
-            input['type'] = "File"
+            inp['type'] = "File"
         else:
-            input['type'] = "String"
+            inp['type'] = "String"
         if trait_handler.minlen != 0:
-            input['min-list-entries'] = trait_handler.minlen
+            inp['min-list-entries'] = trait_handler.minlen
         if trait_handler.maxlen != six.MAXSIZE:
-            input['max-list-entries'] = trait_handler.maxlen
+            inp['max-list-entries'] = trait_handler.maxlen
 
     # Deal with multi-input
     if handler_type == "InputMultiObject":
-        input['type'] = "File"
-        input['list'] = True
+        inp['type'] = "File"
+        inp['list'] = True
 
-    input['value-key'] = "[" + input_name.upper(
+    inp['value-key'] = "[" + input_name.upper(
     ) + "]"  # assumes that input names are unique
 
     # Add the command line flag specified by argstr
     # If no argstr is provided and input type is Flag, create a flag from the name
     if spec.argstr and spec.argstr.split("%")[0]:
-        input['command-line-flag'] = spec.argstr.split("%")[0].strip()
-    elif input['type'] == "Flag":
-        input['command-line-flag'] = ("--%s" % input_name + " ").strip()
+        inp['command-line-flag'] = spec.argstr.split("%")[0].strip()
+    elif inp['type'] == "Flag":
+        inp['command-line-flag'] = ("--%s" % input_name + " ").strip()
 
-    input['description'] = get_description_from_spec(inputs, input_name, spec)
+    inp['description'] = get_description_from_spec(inputs, input_name, spec)
     if not (hasattr(spec, "mandatory") and spec.mandatory):
-        input['optional'] = True
+        inp['optional'] = True
     else:
-        input['optional'] = False
+        inp['optional'] = False
     if spec.usedefault:
-        input['default-value'] = spec.default_value()[1]
+        inp['default-value'] = spec.default_value()[1]
 
     try:
         value_choices = trait_handler.values
@@ -284,17 +284,17 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
     else:
         if value_choices is not None:
             if all(isinstance(n, int) for n in value_choices):
-                input['type'] = "Number"
-                input['integer'] = True
+                inp['type'] = "Number"
+                inp['integer'] = True
             elif all(isinstance(n, float) for n in value_choices):
-                input['type'] = "Number"
-            input['value-choices'] = value_choices
+                inp['type'] = "Number"
+            inp['value-choices'] = value_choices
 
     # Set Boolean types to Flag (there is no Boolean type in Boutiques)
-    if input['type'] == "Boolean":
-        input['type'] = "Flag"
+    if inp['type'] == "Boolean":
+        inp['type'] = "Flag"
 
-    return input
+    return inp
 
 
 def get_boutiques_output(outputs, name, spec, interface, tool_inputs):
@@ -400,28 +400,28 @@ def get_boutiques_groups(input_traits):
                 mutex_input_sets.append(group_members)
 
     # Create a dictionary for each one
-    for i in range(0, len(all_or_none_input_sets)):
-        desc_groups.append({'id': "all_or_none_group" + ("_" + str(i + 1) if i != 0 else ""),
-                            'name': "All or none group" + (" " + str(i + 1) if i != 0 else ""),
-                            'members': list(all_or_none_input_sets[i]),
+    for i, inp_set in enumerate(all_or_none_input_sets, 1):
+        desc_groups.append({'id': "all_or_none_group" + ("_" + str(i) if i != 1 else ""),
+                            'name': "All or none group" + (" " + str(i) if i != 1 else ""),
+                            'members': list(inp_set),
                             'all-or-none': True})
 
-    for i in range(0, len(mutex_input_sets)):
-        desc_groups.append({'id': "mutex_group" + ("_" + str(i + 1) if i != 0 else ""),
-                            'name': "Mutex group" + (" " + str(i + 1) if i != 0 else ""),
-                            'members': list(mutex_input_sets[i]),
+    for i, inp_set in enumerate(mutex_input_sets, 1):
+        desc_groups.append({'id': "mutex_group" + ("_" + str(i) if i != 1 else ""),
+                            'name': "Mutex group" + (" " + str(i) if i != 1 else ""),
+                            'members': list(inp_set),
                             'mutually-exclusive': True})
 
     return desc_groups
 
 
-def get_description_from_spec(object, name, spec):
+def get_description_from_spec(obj, name, spec):
     '''
     Generates a description based on the input or output spec.
     '''
     if not spec.desc:
         spec.desc = "No description provided."
-    spec_info = spec.full_info(object, name, None)
+    spec_info = spec.full_info(obj, name, None)
 
     boutiques_description = (spec_info.capitalize(
     ) + ". " + spec.desc.capitalize()).replace("\n", '')

From 63d96be755b3f550fc3db97ff2ac4272b54825ff Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Mon, 18 Mar 2019 17:17:14 -0400
Subject: [PATCH 18/28] added option to supply descriptor tags, changed default
 tool version to 1.0.0, added logic to deal with 0/1 booleans and tuples,
 added list separator and flag separator checks

---
 nipype/utils/nipype2boutiques.py | 59 +++++++++++++++++++++++++++-----
 1 file changed, 50 insertions(+), 9 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index e5b91b0ea7..6f2988c4ba 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -20,7 +20,7 @@
 
 def generate_boutiques_descriptor(
         module, interface_name, container_image, container_type, container_index=None,
-        verbose=False, save=False, save_path=None, author=None, ignore_inputs=None):
+        verbose=False, save=False, save_path=None, author=None, ignore_inputs=None, tags=None):
     '''
     Returns a JSON string containing a JSON Boutiques description of a Nipype interface.
     Arguments:
@@ -34,6 +34,8 @@ def generate_boutiques_descriptor(
     * save_path: file path for the saved descriptor (defaults to name of the interface in current directory)
     * author: author of the tool (required for publishing)
     * ignore_inputs: list of interface inputs to not include in the descriptor
+    * tags: JSON object containing tags to include in the descriptor, e.g. "{/"key1/": /"value1/"}"
+            (note: the tags 'domain:neuroinformatics' and 'interface-type:nipype' are included by default)
     '''
 
     if not module:
@@ -64,7 +66,7 @@ def generate_boutiques_descriptor(
     tool_desc['inputs'] = []
     tool_desc['output-files'] = []
     tool_desc['groups'] = []
-    tool_desc['tool-version'] = interface.version if interface.version is not None else "No version provided."
+    tool_desc['tool-version'] = interface.version if interface.version is not None else "1.0.0"
     tool_desc['schema-version'] = '0.5'
     if container_image:
         tool_desc['container-image'] = {}
@@ -120,6 +122,24 @@ def generate_boutiques_descriptor(
         if output['path-template'] == "":
             fill_in_missing_output_path(output, output['name'], tool_desc['inputs'])
 
+    # Add tags
+    desc_tags = {
+        'domain': 'neuroinformatics',
+        'source': 'nipype-interface'
+    }
+
+    if tags is not None:
+        tags_dict = json.loads(tags)
+        for k, v in tags_dict.items():
+            if k in desc_tags:
+                if not isinstance(desc_tags[k], list):
+                    desc_tags[k] = [desc_tags[k]]
+                desc_tags[k].append(v)
+            else:
+                desc_tags[k] = v
+
+    tool_desc['tags'] = desc_tags
+
     # Remove the extra space at the end of the command line
     tool_desc['command-line'] = tool_desc['command-line'].strip()
 
@@ -219,7 +239,13 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
     elif handler_type == "Float":
         inp['type'] = "Number"
     elif handler_type == "Bool":
-        inp['type'] = "Flag"
+        if spec.argstr and len(spec.argstr.split("=")) > 1 and (spec.argstr.split("=")[1] == '0' or spec.argstr.split("=")[1] == '1'):
+            inp['type'] = "Number"
+            inp['integer'] = True
+            inp['minimum'] = 0
+            inp['maximum'] = 1
+        else:
+            inp['type'] = "Flag"
     else:
         inp['type'] = "String"
 
@@ -253,6 +279,21 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
             inp['min-list-entries'] = trait_handler.minlen
         if trait_handler.maxlen != six.MAXSIZE:
             inp['max-list-entries'] = trait_handler.maxlen
+        if spec.sep:
+            inp['list-separator'] = spec.sep
+
+    if handler_type == "Tuple":
+        inp['list'] = True
+        inp['min-list-entries'] = len(spec.default)
+        inp['max-list-entries'] = len(spec.default)
+        input_type = type(spec.default[0]).__name__
+        if input_type == 'int':
+            inp['type'] = "Number"
+            inp['integer'] = True
+        elif input_type == 'float':
+            inp['type'] = "Number"
+        else:
+            inp['type'] = "String"
 
     # Deal with multi-input
     if handler_type == "InputMultiObject":
@@ -264,8 +305,12 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
 
     # Add the command line flag specified by argstr
     # If no argstr is provided and input type is Flag, create a flag from the name
-    if spec.argstr and spec.argstr.split("%")[0]:
-        inp['command-line-flag'] = spec.argstr.split("%")[0].strip()
+    if spec.argstr:
+        if "=" in spec.argstr:
+            inp['command-line-flag'] = spec.argstr.split("=")[0].strip()
+            inp['command-line-flag-separator'] = "="
+        elif spec.argstr.split("%")[0]:
+            inp['command-line-flag'] = spec.argstr.split("%")[0].strip()
     elif inp['type'] == "Flag":
         inp['command-line-flag'] = ("--%s" % input_name + " ").strip()
 
@@ -290,10 +335,6 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
                 inp['type'] = "Number"
             inp['value-choices'] = value_choices
 
-    # Set Boolean types to Flag (there is no Boolean type in Boutiques)
-    if inp['type'] == "Boolean":
-        inp['type'] = "Flag"
-
     return inp
 
 

From 1e15b9989f2498e698294532c1a0703596c7b3e2 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Tue, 19 Mar 2019 22:48:42 -0400
Subject: [PATCH 19/28] added method to take into account the order of
 positional command line args

---
 nipype/utils/nipype2boutiques.py | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 6f2988c4ba..c5280d2d45 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -140,6 +140,9 @@ def generate_boutiques_descriptor(
 
     tool_desc['tags'] = desc_tags
 
+    # Check for positional arguments and reorder command line args if necessary
+    tool_desc['command-line'] = reorder_cmd_line_args(tool_desc['command-line'], interface, ignore_inputs)
+
     # Remove the extra space at the end of the command line
     tool_desc['command-line'] = tool_desc['command-line'].strip()
 
@@ -505,3 +508,31 @@ def generate_custom_inputs(desc_inputs):
             for value in desc_input['value-choices']:
                 custom_input_dicts.append({desc_input['id']: value})
     return custom_input_dicts
+
+
+def reorder_cmd_line_args(cmd_line, interface, ignore_inputs=None):
+    '''
+    Generates a new command line with the positional arguments in the correct order
+    '''
+    interface_name = cmd_line.split()[0]
+    positional_arg_dict = {}
+    positional_args = []
+    non_positional_args = []
+
+    for name, spec in sorted(interface.inputs.traits(transient=None).items()):
+        if ignore_inputs is not None and name in ignore_inputs:
+            continue
+        value_key = "[" + name.upper() + "]"
+        if spec.position is not None:
+            positional_arg_dict[spec.position] = value_key
+        else:
+            non_positional_args.append(value_key)
+
+    last_arg = None
+    for item in sorted(positional_arg_dict.items()):
+        if item[0] == -1:
+            last_arg = item[1]
+            continue
+        positional_args.append(item[1])
+
+    return interface_name + " " + " ".join(positional_args) + " " + ((last_arg + " ") if last_arg else "") + " ".join(non_positional_args)

From f0a11b835ede75463ee50745896d60afc0d962b2 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Wed, 27 Mar 2019 17:02:40 -0400
Subject: [PATCH 20/28] added methods to generate command line flag and
 generate a boutiques output from a Nipype input spec, code style fixes, some
 refactoring and improvements

---
 nipype/utils/nipype2boutiques.py | 169 +++++++++++++++++++------------
 1 file changed, 103 insertions(+), 66 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index c5280d2d45..981c8d0cb3 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -9,6 +9,7 @@
 # Limitations:
 #   * Optional outputs, i.e. outputs that not always produced, may not be detected. They will, however, still be listed
 #     with a placeholder for the path template (either a value key or the output ID) that should be verified and corrected.
+#   * Still need to add some fields to the descriptor manually, e.g. url, descriptor-url, path-template-stripped-extensions, etc.
 
 import os
 import sys
@@ -77,28 +78,34 @@ def generate_boutiques_descriptor(
 
     # Generates tool inputs
     for name, spec in sorted(interface.inputs.traits(transient=None).items()):
-        inp = get_boutiques_input(inputs, interface, name, spec, verbose, ignore_inputs=ignore_inputs)
-        # Handle compound inputs (inputs that can be of multiple types and are mutually exclusive)
-        if inp is None:
+        # Skip ignored inputs
+        if ignore_inputs is not None and name in ignore_inputs:
             continue
-        if isinstance(inp, list):
-            mutex_group_members = []
-            tool_desc['command-line'] += inp[0]['value-key'] + " "
-            for i in inp:
-                tool_desc['inputs'].append(i)
-                mutex_group_members.append(i['id'])
-                if verbose:
-                    print("-> Adding input " + i['name'])
-            # Put inputs into a mutually exclusive group
-            tool_desc['groups'].append({'id': inp[0]['id'] + "_group",
-                                        'name': inp[0]['name'] + " group",
-                                        'members': mutex_group_members,
-                                        'mutually-exclusive': True})
+        # If spec has a name source, this means it actually represents an output, so create a
+        # Boutiques output from it
+        elif spec.name_source and spec.name_template:
+            tool_desc['output-files'].append(get_boutiques_output_from_inp(inputs, spec, name))
         else:
-            tool_desc['inputs'].append(inp)
-            tool_desc['command-line'] += inp['value-key'] + " "
-            if verbose:
-                print("-> Adding input " + inp['name'])
+            inp = get_boutiques_input(inputs, interface, name, spec, verbose, ignore_inputs=ignore_inputs)
+            # Handle compound inputs (inputs that can be of multiple types and are mutually exclusive)
+            if isinstance(inp, list):
+                mutex_group_members = []
+                tool_desc['command-line'] += inp[0]['value-key'] + " "
+                for i in inp:
+                    tool_desc['inputs'].append(i)
+                    mutex_group_members.append(i['id'])
+                    if verbose:
+                        print("-> Adding input " + i['name'])
+                # Put inputs into a mutually exclusive group
+                tool_desc['groups'].append({'id': inp[0]['id'] + "_group",
+                                            'name': inp[0]['name'] + " group",
+                                            'members': mutex_group_members,
+                                            'mutually-exclusive': True})
+            else:
+                tool_desc['inputs'].append(inp)
+                tool_desc['command-line'] += inp['value-key'] + " "
+                if verbose:
+                    print("-> Adding input " + inp['name'])
 
     # Generates input groups
     tool_desc['groups'] += get_boutiques_groups(interface.inputs.traits(transient=None).items())
@@ -148,7 +155,7 @@ def generate_boutiques_descriptor(
 
     # Save descriptor to a file
     if save:
-        path = save_path if save_path is not None else os.path.join(os.getcwd(), interface_name + '.json')
+        path = save_path or os.path.join(os.getcwd(), interface_name + '.json')
         with open(path, 'w') as outfile:
             json.dump(tool_desc, outfile, indent=4, separators=(',', ': '))
         if verbose:
@@ -200,15 +207,9 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
     Assumes that:
       * Input names are unique.
     """
-
-    # If spec has a name source, means it's an output, so skip it here.
-    # Also skip any ignored inputs
-    if spec.name_source or ignore_inputs is not None and input_name in ignore_inputs:
-        return None
-
     inp = {}
 
-    if input_number is not None and input_number != 0:  # No need to append a number to the first of a list of compound inputs
+    if input_number:  # No need to append a number to the first of a list of compound inputs
         inp['id'] = input_name + "_" + str(input_number + 1)
     else:
         inp['id'] = input_name
@@ -302,20 +303,18 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
     if handler_type == "InputMultiObject":
         inp['type'] = "File"
         inp['list'] = True
+        if spec.sep:
+            inp['list-separator'] = spec.sep
 
     inp['value-key'] = "[" + input_name.upper(
     ) + "]"  # assumes that input names are unique
 
-    # Add the command line flag specified by argstr
-    # If no argstr is provided and input type is Flag, create a flag from the name
-    if spec.argstr:
-        if "=" in spec.argstr:
-            inp['command-line-flag'] = spec.argstr.split("=")[0].strip()
-            inp['command-line-flag-separator'] = "="
-        elif spec.argstr.split("%")[0]:
-            inp['command-line-flag'] = spec.argstr.split("%")[0].strip()
-    elif inp['type'] == "Flag":
-        inp['command-line-flag'] = ("--%s" % input_name + " ").strip()
+    flag, flag_sep = get_command_line_flag(spec, inp['type'] == "Flag", input_name)
+
+    if flag is not None:
+        inp['command-line-flag'] = flag
+    if flag_sep is not None:
+        inp['command-line-flag-separator'] = flag_sep
 
     inp['description'] = get_description_from_spec(inputs, input_name, spec)
     if not (hasattr(spec, "mandatory") and spec.mandatory):
@@ -384,42 +383,32 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs):
         output_value = None
     except AttributeError:
         output_value = None
+    except KeyError:
+        output_value = None
 
     # Handle multi-outputs
-    if isinstance(output_value, list):
+    if isinstance(output_value, list) or type(spec.handler).__name__ == "OutputMultiObject":
         output['list'] = True
-        # Check if all extensions are the same
-        extensions = []
-        for val in output_value:
-            extensions.append(os.path.splitext(val)[1])
-        # If extensions all the same, set path template as wildcard + extension
-        # Otherwise just use a wildcard
-        if len(set(extensions)) == 1:
-            output['path-template'] = "*" + extensions[0]
-        else:
-            output['path-template'] = "*"
-        return output
+        if output_value:
+            # Check if all extensions are the same
+            extensions = []
+            for val in output_value:
+                extensions.append(os.path.splitext(val)[1])
+            # If extensions all the same, set path template as wildcard + extension
+            # Otherwise just use a wildcard
+            if len(set(extensions)) == 1:
+                output['path-template'] = "*" + extensions[0]
+            else:
+                output['path-template'] = "*"
+            return output
 
     # If an output value is defined, use its relative path, if one exists.
-    # If no relative path, look for an input with the same name containing a name source
-    # and name template. Otherwise, put blank string as placeholder and try to fill it on
+    # Otherwise, put blank string as placeholder and try to fill it on
     # another iteration.
-    output['path-template'] = ""
-
     if output_value:
         output['path-template'] = os.path.relpath(output_value)
     else:
-        for inp_name, inp_spec in sorted(interface.inputs.traits(transient=None).items()):
-            if inp_name == name and inp_spec.name_source and inp_spec.name_template:
-                if isinstance(inp_spec.name_source, list):
-                    source = inp_spec.name_source[0]
-                else:
-                    source = inp_spec.name_source
-                output['path-template'] = inp_spec.name_template.replace("%s", "[" + source.upper() + "]")
-                output['value-key'] = "[" + name.upper() + "]"
-                if inp_spec.argstr and inp_spec.argstr.split("%")[0]:
-                    output['command-line-flag'] = inp_spec.argstr.split("%")[0].strip()
-                break
+        output['path-template'] = ""
 
     return output
 
@@ -535,4 +524,52 @@ def reorder_cmd_line_args(cmd_line, interface, ignore_inputs=None):
             continue
         positional_args.append(item[1])
 
-    return interface_name + " " + " ".join(positional_args) + " " + ((last_arg + " ") if last_arg else "") + " ".join(non_positional_args)
+    return interface_name + " " +\
+           ((" ".join(positional_args) + " ") if len(positional_args) > 0 else "") +\
+           ((last_arg + " ") if last_arg else "") +\
+           " ".join(non_positional_args)
+
+
+def get_command_line_flag(input_spec, is_flag_type=False, input_name=None):
+    '''
+    Generates the command line flag for a given input
+    '''
+    flag, flag_sep = None, None
+    if input_spec.argstr:
+        if "=" in input_spec.argstr:
+            flag = input_spec.argstr.split("=")[0].strip()
+            flag_sep = "="
+        elif input_spec.argstr.split("%")[0]:
+            flag = input_spec.argstr.split("%")[0].strip()
+    elif is_flag_type:
+        flag = ("--%s" % input_name + " ").strip()
+    return flag, flag_sep
+
+
+def get_boutiques_output_from_inp(inputs, inp_spec, inp_name):
+    '''
+    Takes a Nipype input representing an output file and generates a Boutiques output for it
+    '''
+    output = {}
+    output['name'] = inp_name.replace('_', ' ').capitalize()
+    output['id'] = inp_name
+    output['optional'] = True
+    output['description'] = get_description_from_spec(inputs, inp_name, inp_spec)
+    if not (hasattr(inp_spec, "mandatory") and inp_spec.mandatory):
+        output['optional'] = True
+    else:
+        output['optional'] = False
+    if inp_spec.usedefault:
+        output['default-value'] = inp_spec.default_value()[1]
+    if isinstance(inp_spec.name_source, list):
+        source = inp_spec.name_source[0]
+    else:
+        source = inp_spec.name_source
+    output['path-template'] = inp_spec.name_template.replace("%s", "[" + source.upper() + "]")
+    output['value-key'] = "[" + inp_name.upper() + "]"
+    flag, flag_sep = get_command_line_flag(inp_spec)
+    if flag is not None:
+        output['command-line-flag'] = flag
+    if flag_sep is not None:
+        output['command-line-flag-separator'] = flag_sep
+    return output

From b4b2de077fc94978c30c70355252d8ce9ea68775 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Wed, 27 Mar 2019 21:20:26 -0400
Subject: [PATCH 21/28] updated nipypecli, fixed code style

---
 nipype/scripts/cli.py            |  61 +++++++-----
 nipype/utils/nipype2boutiques.py | 166 +++++++++++++++++++------------
 2 files changed, 139 insertions(+), 88 deletions(-)

diff --git a/nipype/scripts/cli.py b/nipype/scripts/cli.py
index 59d8672cfb..482f359aae 100644
--- a/nipype/scripts/cli.py
+++ b/nipype/scripts/cli.py
@@ -211,48 +211,55 @@ def convert():
     help="JSON file name where the Boutiques descriptor will be "
     "written.")
 @click.option(
-    "-t",
-    "--ignored-template-inputs",
+    "-c",
+    "--container-image",
+    required=True,
     type=str,
-    multiple=True,
-    help="Interface inputs ignored in path template creations.")
+    help="Name of the container image where the tool is installed.")
 @click.option(
-    "-d",
-    "--docker-image",
+    "-p",
+    "--container-type",
+    required=True,
     type=str,
-    help="Name of the Docker image where the Nipype interface is "
-    "available.")
+    help="Type of container image (Docker or Singularity).")
 @click.option(
-    "-r",
-    "--docker-index",
+    "-x",
+    "--container-index",
     type=str,
-    help="Docker index where the Docker image is stored (e.g. "
+    help="Optional index where the image is available (e.g. "
     "http://index.docker.io).")
 @click.option(
-    "-n",
-    "--ignore-template-numbers",
-    is_flag=True,
-    flag_value=True,
-    help="Ignore all numbers in path template creations.")
+    "-g",
+    "--ignore-inputs",
+    type=str,
+    multiple=True,
+    help="List of interface inputs to not include in the descriptor.")
 @click.option(
     "-v",
     "--verbose",
     is_flag=True,
     flag_value=True,
-    help="Enable verbose output.")
-def boutiques(interface, module, output, ignored_template_inputs, docker_image,
-              docker_index, ignore_template_numbers, verbose):
+    help="Print information messages.")
+@click.option(
+    "-a",
+    "--author",
+    type=str,
+    help="Author of the tool (required for publishing).")
+@click.option(
+    "-t",
+    "--tags",
+    type=str,
+    help="JSON string containing tags to include in the descriptor,"
+         "e.g. \"{\"key1\": \"value1\"}\"")
+def boutiques(module, interface, container_image, container_type, output,
+              container_index, verbose, author, ignore_inputs, tags):
     """Nipype to Boutiques exporter.
 
     See Boutiques specification at https://github.com/boutiques/schema.
     """
     from nipype.utils.nipype2boutiques import generate_boutiques_descriptor
 
-    # Generates JSON string
-    json_string = generate_boutiques_descriptor(
-        module, interface, ignored_template_inputs, docker_image, docker_index,
-        verbose, ignore_template_numbers)
-
-    # Writes JSON string to file
-    with open(output, 'w') as f:
-        f.write(json_string)
+    # Generates JSON string and saves it to file
+    generate_boutiques_descriptor(
+        module, interface, container_image, container_type, container_index,
+        verbose, True, output, author, ignore_inputs, tags)
diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 981c8d0cb3..a9500a71a8 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -3,13 +3,18 @@
                         absolute_import)
 
 from builtins import str, open, bytes
-# This tool exports a Nipype interface in the Boutiques (https://github.com/boutiques) JSON format.
-# Boutiques tools can be imported in CBRAIN (https://github.com/aces/cbrain) among other platforms.
+# This tool exports a Nipype interface in the Boutiques
+# (https://github.com/boutiques) JSON format. Boutiques tools
+# can be imported in CBRAIN (https://github.com/aces/cbrain)
+# among other platforms.
 #
 # Limitations:
-#   * Optional outputs, i.e. outputs that not always produced, may not be detected. They will, however, still be listed
-#     with a placeholder for the path template (either a value key or the output ID) that should be verified and corrected.
-#   * Still need to add some fields to the descriptor manually, e.g. url, descriptor-url, path-template-stripped-extensions, etc.
+#   * Optional outputs, i.e. outputs that not always produced, may not be
+#     detected. They will, however, still be listed with a placeholder for
+#     the path template (either a value key or the output ID) that should
+#     be verified and corrected.
+#   * Still need to add some fields to the descriptor manually, e.g. url,
+#     descriptor-url, path-template-stripped-extensions, etc.
 
 import os
 import sys
@@ -20,10 +25,12 @@
 
 
 def generate_boutiques_descriptor(
-        module, interface_name, container_image, container_type, container_index=None,
-        verbose=False, save=False, save_path=None, author=None, ignore_inputs=None, tags=None):
+        module, interface_name, container_image, container_type,
+        container_index=None, verbose=False, save=False, save_path=None,
+        author=None, ignore_inputs=None, tags=None):
     '''
-    Returns a JSON string containing a JSON Boutiques description of a Nipype interface.
+    Returns a JSON string containing a JSON Boutiques description of a
+    Nipype interface.
     Arguments:
     * module: module where the Nipype interface is declared.
     * interface_name: name of Nipype interface.
@@ -32,11 +39,13 @@ def generate_boutiques_descriptor(
     * container_index: optional index where the image is available
     * verbose: print information messages
     * save: True if you want to save descriptor to a file
-    * save_path: file path for the saved descriptor (defaults to name of the interface in current directory)
+    * save_path: file path for the saved descriptor (defaults to name of the
+      interface in current directory)
     * author: author of the tool (required for publishing)
     * ignore_inputs: list of interface inputs to not include in the descriptor
-    * tags: JSON object containing tags to include in the descriptor, e.g. "{/"key1/": /"value1/"}"
-            (note: the tags 'domain:neuroinformatics' and 'interface-type:nipype' are included by default)
+    * tags: JSON object containing tags to include in the descriptor,
+      e.g. "{\"key1\": \"value1\"}" (note: the tags 'domain:neuroinformatics'
+      and 'interface-type:nipype' are included by default)
     '''
 
     if not module:
@@ -62,12 +71,15 @@ def generate_boutiques_descriptor(
     tool_desc['author'] = "Nipype (interface)"
     if author is not None:
         tool_desc['author'] = tool_desc['author'] + ", " + author + " (tool)"
-    tool_desc[
-        'description'] = interface_name + ", as implemented in Nipype (module: " + module_name + ", interface: " + interface_name + ")."
+    tool_desc['description'] = (interface_name +
+                                ", as implemented in Nipype (module: " +
+                                module_name + ", interface: " +
+                                interface_name + ").")
     tool_desc['inputs'] = []
     tool_desc['output-files'] = []
     tool_desc['groups'] = []
-    tool_desc['tool-version'] = interface.version if interface.version is not None else "1.0.0"
+    tool_desc['tool-version'] = interface.version \
+        if interface.version is not None else "1.0.0"
     tool_desc['schema-version'] = '0.5'
     if container_image:
         tool_desc['container-image'] = {}
@@ -81,13 +93,15 @@ def generate_boutiques_descriptor(
         # Skip ignored inputs
         if ignore_inputs is not None and name in ignore_inputs:
             continue
-        # If spec has a name source, this means it actually represents an output, so create a
-        # Boutiques output from it
+        # If spec has a name source, this means it actually represents an
+        # output, so create a Boutiques output from it
         elif spec.name_source and spec.name_template:
-            tool_desc['output-files'].append(get_boutiques_output_from_inp(inputs, spec, name))
+            tool_desc['output-files']\
+                .append(get_boutiques_output_from_inp(inputs, spec, name))
         else:
-            inp = get_boutiques_input(inputs, interface, name, spec, verbose, ignore_inputs=ignore_inputs)
-            # Handle compound inputs (inputs that can be of multiple types and are mutually exclusive)
+            inp = get_boutiques_input(inputs, interface, name, spec, verbose)
+            # Handle compound inputs (inputs that can be of multiple types
+            # and are mutually exclusive)
             if isinstance(inp, list):
                 mutex_group_members = []
                 tool_desc['command-line'] += inp[0]['value-key'] + " "
@@ -108,7 +122,8 @@ def generate_boutiques_descriptor(
                     print("-> Adding input " + inp['name'])
 
     # Generates input groups
-    tool_desc['groups'] += get_boutiques_groups(interface.inputs.traits(transient=None).items())
+    tool_desc['groups'] +=\
+        get_boutiques_groups(interface.inputs.traits(transient=None).items())
     if len(tool_desc['groups']) == 0:
         del tool_desc['groups']
 
@@ -127,7 +142,8 @@ def generate_boutiques_descriptor(
     # Fill in all missing output paths
     for output in tool_desc['output-files']:
         if output['path-template'] == "":
-            fill_in_missing_output_path(output, output['name'], tool_desc['inputs'])
+            fill_in_missing_output_path(output, output['name'],
+                                        tool_desc['inputs'])
 
     # Add tags
     desc_tags = {
@@ -148,7 +164,8 @@ def generate_boutiques_descriptor(
     tool_desc['tags'] = desc_tags
 
     # Check for positional arguments and reorder command line args if necessary
-    tool_desc['command-line'] = reorder_cmd_line_args(tool_desc['command-line'], interface, ignore_inputs)
+    tool_desc['command-line'] = reorder_cmd_line_args(
+        tool_desc['command-line'], interface, ignore_inputs)
 
     # Remove the extra space at the end of the command line
     tool_desc['command-line'] = tool_desc['command-line'].strip()
@@ -161,16 +178,19 @@ def generate_boutiques_descriptor(
         if verbose:
             print("-> Descriptor saved to file " + outfile.name)
 
-    print("NOTE: Descriptors produced by this script may not entirely conform to the Nipype interface "
-          "specs. Please check that the descriptor is correct before using it.")
+    print("NOTE: Descriptors produced by this script may not entirely conform "
+          "to the Nipype interface specs. Please check that the descriptor is "
+          "correct before using it.")
     return json.dumps(tool_desc, indent=4, separators=(',', ': '))
 
 
 def generate_tool_outputs(outputs, interface, tool_desc, verbose, first_run):
     for name, spec in sorted(outputs.traits(transient=None).items()):
-        output = get_boutiques_output(outputs, name, spec, interface, tool_desc['inputs'])
-        # If this is the first time we are generating outputs, add the full output to the descriptor.
-        # Otherwise, find the existing output and update its path template if it's still undefined.
+        output = get_boutiques_output(outputs, name, spec, interface,
+                                      tool_desc['inputs'])
+        # If this is the first time we are generating outputs, add the full
+        # output to the descriptor. Otherwise, find the existing output and
+        # update its path template if it's still undefined.
         if first_run:
             tool_desc['output-files'].append(output)
             if output.get('value-key'):
@@ -179,20 +199,23 @@ def generate_tool_outputs(outputs, interface, tool_desc, verbose, first_run):
                 print("-> Adding output " + output['name'])
         else:
             for existing_output in tool_desc['output-files']:
-                if output['id'] == existing_output['id'] and existing_output['path-template'] == "":
+                if (output['id'] == existing_output['id'] and
+                        existing_output['path-template'] == ""):
                     existing_output['path-template'] = output['path-template']
                     break
-            if output.get('value-key') and output['value-key'] not in tool_desc['command-line']:
+            if (output.get('value-key') and
+                    output['value-key'] not in tool_desc['command-line']):
                 tool_desc['command-line'] += output['value-key'] + " "
 
     if len(tool_desc['output-files']) == 0:
         raise Exception("Tool has no output.")
 
 
-def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=None,
-                        input_number=None, ignore_inputs=None):
+def get_boutiques_input(inputs, interface, input_name, spec, verbose,
+                        handler=None, input_number=None):
     """
-    Returns a dictionary containing the Boutiques input corresponding to a Nipype intput.
+    Returns a dictionary containing the Boutiques input corresponding
+    to a Nipype input.
 
     Args:
       * inputs: inputs of the Nipype interface.
@@ -200,16 +223,18 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
       * input_name: name of the Nipype input.
       * spec: Nipype input spec.
       * verbose: print information messages.
-      * handler: used when handling compound inputs, which don't have their own input spec
-      * input_number: used when handling compound inputs to assign each a unique ID
-      * ignore_inputs: list of interface inputs to not include in the descriptor
+      * handler: used when handling compound inputs, which don't have their
+        own input spec
+      * input_number: used when handling compound inputs to assign each a
+        unique ID
 
     Assumes that:
       * Input names are unique.
     """
     inp = {}
 
-    if input_number:  # No need to append a number to the first of a list of compound inputs
+    # No need to append a number to the first of a list of compound inputs
+    if input_number:
         inp['id'] = input_name + "_" + str(input_number + 1)
     else:
         inp['id'] = input_name
@@ -243,7 +268,9 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
     elif handler_type == "Float":
         inp['type'] = "Number"
     elif handler_type == "Bool":
-        if spec.argstr and len(spec.argstr.split("=")) > 1 and (spec.argstr.split("=")[1] == '0' or spec.argstr.split("=")[1] == '1'):
+        if (spec.argstr and len(spec.argstr.split("=")) > 1 and
+                (spec.argstr.split("=")[1] == '0'
+                 or spec.argstr.split("=")[1] == '1')):
             inp['type'] = "Number"
             inp['integer'] = True
             inp['minimum'] = 0
@@ -309,7 +336,8 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
     inp['value-key'] = "[" + input_name.upper(
     ) + "]"  # assumes that input names are unique
 
-    flag, flag_sep = get_command_line_flag(spec, inp['type'] == "Flag", input_name)
+    flag, flag_sep = get_command_line_flag(spec, inp['type'] == "Flag",
+                                           input_name)
 
     if flag is not None:
         inp['command-line-flag'] = flag
@@ -342,14 +370,16 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose, handler=No
 
 def get_boutiques_output(outputs, name, spec, interface, tool_inputs):
     """
-    Returns a dictionary containing the Boutiques output corresponding to a Nipype output.
+    Returns a dictionary containing the Boutiques output corresponding
+    to a Nipype output.
 
     Args:
       * outputs: outputs of the Nipype interface.
       * name: name of the Nipype output.
       * spec: Nipype output spec.
       * interface: Nipype interface.
-      * tool_inputs: list of tool inputs (as produced by method get_boutiques_input).
+      * tool_inputs: list of tool inputs (as produced by method
+        get_boutiques_input).
 
     Assumes that:
       * Output names are unique.
@@ -370,8 +400,10 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs):
     output['id'] = name if unique_id else name + '_outfile'
 
     output['path-template'] = ""
-    output[
-        'optional'] = True  # no real way to determine if an output is always produced, regardless of the input values.
+
+    # No real way to determine if an output is always
+    # produced, regardless of the input values.
+    output['optional'] = True
 
     output['description'] = get_description_from_spec(outputs, name, spec)
 
@@ -387,15 +419,16 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs):
         output_value = None
 
     # Handle multi-outputs
-    if isinstance(output_value, list) or type(spec.handler).__name__ == "OutputMultiObject":
+    if (isinstance(output_value, list) or
+            type(spec.handler).__name__ == "OutputMultiObject"):
         output['list'] = True
         if output_value:
             # Check if all extensions are the same
             extensions = []
             for val in output_value:
                 extensions.append(os.path.splitext(val)[1])
-            # If extensions all the same, set path template as wildcard + extension
-            # Otherwise just use a wildcard
+            # If extensions all the same, set path template as
+            # wildcard + extension. Otherwise just use a wildcard
             if len(set(extensions)) == 1:
                 output['path-template'] = "*" + extensions[0]
             else:
@@ -415,7 +448,8 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs):
 
 def get_boutiques_groups(input_traits):
     """
-    Returns a list of dictionaries containing Boutiques groups for the mutually exclusive and all-or-none Nipype inputs.
+    Returns a list of dictionaries containing Boutiques groups for the mutually
+    exclusive and all-or-none Nipype inputs.
     """
     desc_groups = []
     all_or_none_input_sets = []
@@ -434,14 +468,18 @@ def get_boutiques_groups(input_traits):
 
     # Create a dictionary for each one
     for i, inp_set in enumerate(all_or_none_input_sets, 1):
-        desc_groups.append({'id': "all_or_none_group" + ("_" + str(i) if i != 1 else ""),
-                            'name': "All or none group" + (" " + str(i) if i != 1 else ""),
+        desc_groups.append({'id': "all_or_none_group" +
+                                  ("_" + str(i) if i != 1 else ""),
+                            'name': "All or none group" +
+                                    (" " + str(i) if i != 1 else ""),
                             'members': list(inp_set),
                             'all-or-none': True})
 
     for i, inp_set in enumerate(mutex_input_sets, 1):
-        desc_groups.append({'id': "mutex_group" + ("_" + str(i) if i != 1 else ""),
-                            'name': "Mutex group" + (" " + str(i) if i != 1 else ""),
+        desc_groups.append({'id': "mutex_group" +
+                                  ("_" + str(i) if i != 1 else ""),
+                            'name': "Mutex group" +
+                                    (" " + str(i) if i != 1 else ""),
                             'members': list(inp_set),
                             'mutually-exclusive': True})
 
@@ -485,9 +523,10 @@ def fill_in_missing_output_path(output, output_name, tool_inputs):
 
 def generate_custom_inputs(desc_inputs):
     '''
-    Generates a bunch of custom input dictionaries in order to generate as many outputs as possible
-    (to get their path templates)
-    Currently only works with flag inputs and inputs with defined value choices.
+    Generates a bunch of custom input dictionaries in order to generate
+    as many outputs as possible (to get their path templates).
+    Currently only works with flag inputs and inputs with defined value
+    choices.
     '''
     custom_input_dicts = []
     for desc_input in desc_inputs:
@@ -501,7 +540,8 @@ def generate_custom_inputs(desc_inputs):
 
 def reorder_cmd_line_args(cmd_line, interface, ignore_inputs=None):
     '''
-    Generates a new command line with the positional arguments in the correct order
+    Generates a new command line with the positional arguments in the
+    correct order
     '''
     interface_name = cmd_line.split()[0]
     positional_arg_dict = {}
@@ -524,10 +564,11 @@ def reorder_cmd_line_args(cmd_line, interface, ignore_inputs=None):
             continue
         positional_args.append(item[1])
 
-    return interface_name + " " +\
-           ((" ".join(positional_args) + " ") if len(positional_args) > 0 else "") +\
-           ((last_arg + " ") if last_arg else "") +\
-           " ".join(non_positional_args)
+    return (interface_name + " " +
+            ((" ".join(positional_args) + " ")
+                if len(positional_args) > 0 else "") +
+            ((last_arg + " ") if last_arg else "") +
+            " ".join(non_positional_args))
 
 
 def get_command_line_flag(input_spec, is_flag_type=False, input_name=None):
@@ -548,13 +589,15 @@ def get_command_line_flag(input_spec, is_flag_type=False, input_name=None):
 
 def get_boutiques_output_from_inp(inputs, inp_spec, inp_name):
     '''
-    Takes a Nipype input representing an output file and generates a Boutiques output for it
+    Takes a Nipype input representing an output file and generates a
+    Boutiques output for it
     '''
     output = {}
     output['name'] = inp_name.replace('_', ' ').capitalize()
     output['id'] = inp_name
     output['optional'] = True
-    output['description'] = get_description_from_spec(inputs, inp_name, inp_spec)
+    output['description'] = get_description_from_spec(inputs, inp_name,
+                                                      inp_spec)
     if not (hasattr(inp_spec, "mandatory") and inp_spec.mandatory):
         output['optional'] = True
     else:
@@ -565,7 +608,8 @@ def get_boutiques_output_from_inp(inputs, inp_spec, inp_name):
         source = inp_spec.name_source[0]
     else:
         source = inp_spec.name_source
-    output['path-template'] = inp_spec.name_template.replace("%s", "[" + source.upper() + "]")
+    output['path-template'] = inp_spec.name_template.replace(
+        "%s", "[" + source.upper() + "]")
     output['value-key'] = "[" + inp_name.upper() + "]"
     flag, flag_sep = get_command_line_flag(inp_spec)
     if flag is not None:

From ebe7da702d84a405901a2aabb11e5873207b9622 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Thu, 28 Mar 2019 20:47:03 -0400
Subject: [PATCH 22/28] updated nipype2boutiques test

---
 nipype/utils/nipype2boutiques_example.json  | 549 ++++++++++++++++++++
 nipype/utils/tests/test_nipype2boutiques.py |  42 +-
 2 files changed, 582 insertions(+), 9 deletions(-)
 create mode 100644 nipype/utils/nipype2boutiques_example.json

diff --git a/nipype/utils/nipype2boutiques_example.json b/nipype/utils/nipype2boutiques_example.json
new file mode 100644
index 0000000000..45359f49ed
--- /dev/null
+++ b/nipype/utils/nipype2boutiques_example.json
@@ -0,0 +1,549 @@
+{
+    "name": "FLIRT",
+    "command-line": "FLIRT [IN_FILE] [REFERENCE] [OUT_FILE] [OUT_MATRIX_FILE] [ANGLE_REP] [APPLY_ISOXFM] [APPLY_XFM] [BBRSLOPE] [BBRTYPE] [BGVALUE] [BINS] [COARSE_SEARCH] [COST] [COST_FUNC] [DATATYPE] [DISPLAY_INIT] [DOF] [ECHOSPACING] [FIELDMAP] [FIELDMAPMASK] [FINE_SEARCH] [FORCE_SCALING] [IN_MATRIX_FILE] [IN_WEIGHT] [INTERP] [MIN_SAMPLING] [NO_CLAMP] [NO_RESAMPLE] [NO_RESAMPLE_BLUR] [NO_SEARCH] [OUT_LOG] [PADDING_SIZE] [PEDIR] [REF_WEIGHT] [RIGID2D] [SAVE_LOG] [SCHEDULE] [SEARCHR_X] [SEARCHR_Y] [SEARCHR_Z] [SINC_WIDTH] [SINC_WINDOW] [USES_QFORM] [VERBOSE] [WM_SEG] [WMCOORDS] [WMNORMS]",
+    "author": "Nipype (interface), Oxford Centre for Functional MRI of the Brain (FMRIB) (tool)",
+    "description": "FLIRT, as implemented in Nipype (module: nipype.interfaces.fsl, interface: FLIRT).",
+    "inputs": [
+        {
+            "id": "angle_rep",
+            "name": "Angle rep",
+            "type": "String",
+            "value-key": "[ANGLE_REP]",
+            "command-line-flag": "-anglerep",
+            "description": "'quaternion' or 'euler'. Representation of rotation angles.",
+            "optional": true,
+            "value-choices": [
+                "quaternion",
+                "euler"
+            ]
+        },
+        {
+            "id": "apply_isoxfm",
+            "name": "Apply isoxfm",
+            "type": "Number",
+            "value-key": "[APPLY_ISOXFM]",
+            "command-line-flag": "-applyisoxfm",
+            "description": "A float. As applyxfm but forces isotropic resampling.",
+            "optional": true
+        },
+        {
+            "id": "apply_xfm",
+            "name": "Apply xfm",
+            "type": "Flag",
+            "value-key": "[APPLY_XFM]",
+            "command-line-flag": "-applyxfm",
+            "description": "A boolean. Apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header.",
+            "optional": true
+        },
+        {
+            "id": "bbrslope",
+            "name": "Bbrslope",
+            "type": "Number",
+            "value-key": "[BBRSLOPE]",
+            "command-line-flag": "-bbrslope",
+            "description": "A float. Value of bbr slope.",
+            "optional": true
+        },
+        {
+            "id": "bbrtype",
+            "name": "Bbrtype",
+            "type": "String",
+            "value-key": "[BBRTYPE]",
+            "command-line-flag": "-bbrtype",
+            "description": "'signed' or 'global_abs' or 'local_abs'. Type of bbr cost function: signed [default], global_abs, local_abs.",
+            "optional": true,
+            "value-choices": [
+                "signed",
+                "global_abs",
+                "local_abs"
+            ]
+        },
+        {
+            "id": "bgvalue",
+            "name": "Bgvalue",
+            "type": "Number",
+            "value-key": "[BGVALUE]",
+            "command-line-flag": "-setbackground",
+            "description": "A float. Use specified background value for points outside fov.",
+            "optional": true
+        },
+        {
+            "id": "bins",
+            "name": "Bins",
+            "type": "Number",
+            "integer": true,
+            "value-key": "[BINS]",
+            "command-line-flag": "-bins",
+            "description": "An integer (int or long). Number of histogram bins.",
+            "optional": true
+        },
+        {
+            "id": "coarse_search",
+            "name": "Coarse search",
+            "type": "Number",
+            "integer": true,
+            "value-key": "[COARSE_SEARCH]",
+            "command-line-flag": "-coarsesearch",
+            "description": "An integer (int or long). Coarse search delta angle.",
+            "optional": true
+        },
+        {
+            "id": "cost",
+            "name": "Cost",
+            "type": "String",
+            "value-key": "[COST]",
+            "command-line-flag": "-cost",
+            "description": "'mutualinfo' or 'corratio' or 'normcorr' or 'normmi' or 'leastsq' or 'labeldiff' or 'bbr'. Cost function.",
+            "optional": true,
+            "value-choices": [
+                "mutualinfo",
+                "corratio",
+                "normcorr",
+                "normmi",
+                "leastsq",
+                "labeldiff",
+                "bbr"
+            ]
+        },
+        {
+            "id": "cost_func",
+            "name": "Cost func",
+            "type": "String",
+            "value-key": "[COST_FUNC]",
+            "command-line-flag": "-searchcost",
+            "description": "'mutualinfo' or 'corratio' or 'normcorr' or 'normmi' or 'leastsq' or 'labeldiff' or 'bbr'. Cost function.",
+            "optional": true,
+            "value-choices": [
+                "mutualinfo",
+                "corratio",
+                "normcorr",
+                "normmi",
+                "leastsq",
+                "labeldiff",
+                "bbr"
+            ]
+        },
+        {
+            "id": "datatype",
+            "name": "Datatype",
+            "type": "String",
+            "value-key": "[DATATYPE]",
+            "command-line-flag": "-datatype",
+            "description": "'char' or 'short' or 'int' or 'float' or 'double'. Force output data type.",
+            "optional": true,
+            "value-choices": [
+                "char",
+                "short",
+                "int",
+                "float",
+                "double"
+            ]
+        },
+        {
+            "id": "display_init",
+            "name": "Display init",
+            "type": "Flag",
+            "value-key": "[DISPLAY_INIT]",
+            "command-line-flag": "-displayinit",
+            "description": "A boolean. Display initial matrix.",
+            "optional": true
+        },
+        {
+            "id": "dof",
+            "name": "Dof",
+            "type": "Number",
+            "integer": true,
+            "value-key": "[DOF]",
+            "command-line-flag": "-dof",
+            "description": "An integer (int or long). Number of transform degrees of freedom.",
+            "optional": true
+        },
+        {
+            "id": "echospacing",
+            "name": "Echospacing",
+            "type": "Number",
+            "value-key": "[ECHOSPACING]",
+            "command-line-flag": "-echospacing",
+            "description": "A float. Value of epi echo spacing - units of seconds.",
+            "optional": true
+        },
+        {
+            "id": "fieldmap",
+            "name": "Fieldmap",
+            "type": "File",
+            "value-key": "[FIELDMAP]",
+            "command-line-flag": "-fieldmap",
+            "description": "A file name. Fieldmap image in rads/s - must be already registered to the reference image.",
+            "optional": true
+        },
+        {
+            "id": "fieldmapmask",
+            "name": "Fieldmapmask",
+            "type": "File",
+            "value-key": "[FIELDMAPMASK]",
+            "command-line-flag": "-fieldmapmask",
+            "description": "A file name. Mask for fieldmap image.",
+            "optional": true
+        },
+        {
+            "id": "fine_search",
+            "name": "Fine search",
+            "type": "Number",
+            "integer": true,
+            "value-key": "[FINE_SEARCH]",
+            "command-line-flag": "-finesearch",
+            "description": "An integer (int or long). Fine search delta angle.",
+            "optional": true
+        },
+        {
+            "id": "force_scaling",
+            "name": "Force scaling",
+            "type": "Flag",
+            "value-key": "[FORCE_SCALING]",
+            "command-line-flag": "-forcescaling",
+            "description": "A boolean. Force rescaling even for low-res images.",
+            "optional": true
+        },
+        {
+            "id": "in_file",
+            "name": "In file",
+            "type": "File",
+            "value-key": "[IN_FILE]",
+            "command-line-flag": "-in",
+            "description": "An existing file name. Input file.",
+            "optional": false
+        },
+        {
+            "id": "in_matrix_file",
+            "name": "In matrix file",
+            "type": "File",
+            "value-key": "[IN_MATRIX_FILE]",
+            "command-line-flag": "-init",
+            "description": "A file name. Input 4x4 affine matrix.",
+            "optional": true
+        },
+        {
+            "id": "in_weight",
+            "name": "In weight",
+            "type": "File",
+            "value-key": "[IN_WEIGHT]",
+            "command-line-flag": "-inweight",
+            "description": "An existing file name. File for input weighting volume.",
+            "optional": true
+        },
+        {
+            "id": "interp",
+            "name": "Interp",
+            "type": "String",
+            "value-key": "[INTERP]",
+            "command-line-flag": "-interp",
+            "description": "'trilinear' or 'nearestneighbour' or 'sinc' or 'spline'. Final interpolation method used in reslicing.",
+            "optional": true,
+            "value-choices": [
+                "trilinear",
+                "nearestneighbour",
+                "sinc",
+                "spline"
+            ]
+        },
+        {
+            "id": "min_sampling",
+            "name": "Min sampling",
+            "type": "Number",
+            "value-key": "[MIN_SAMPLING]",
+            "command-line-flag": "-minsampling",
+            "description": "A float. Set minimum voxel dimension for sampling.",
+            "optional": true
+        },
+        {
+            "id": "no_clamp",
+            "name": "No clamp",
+            "type": "Flag",
+            "value-key": "[NO_CLAMP]",
+            "command-line-flag": "-noclamp",
+            "description": "A boolean. Do not use intensity clamping.",
+            "optional": true
+        },
+        {
+            "id": "no_resample",
+            "name": "No resample",
+            "type": "Flag",
+            "value-key": "[NO_RESAMPLE]",
+            "command-line-flag": "-noresample",
+            "description": "A boolean. Do not change input sampling.",
+            "optional": true
+        },
+        {
+            "id": "no_resample_blur",
+            "name": "No resample blur",
+            "type": "Flag",
+            "value-key": "[NO_RESAMPLE_BLUR]",
+            "command-line-flag": "-noresampblur",
+            "description": "A boolean. Do not use blurring on downsampling.",
+            "optional": true
+        },
+        {
+            "id": "no_search",
+            "name": "No search",
+            "type": "Flag",
+            "value-key": "[NO_SEARCH]",
+            "command-line-flag": "-nosearch",
+            "description": "A boolean. Set all angular searches to ranges 0 to 0.",
+            "optional": true
+        },
+        {
+            "id": "padding_size",
+            "name": "Padding size",
+            "type": "Number",
+            "integer": true,
+            "value-key": "[PADDING_SIZE]",
+            "command-line-flag": "-paddingsize",
+            "description": "An integer (int or long). For applyxfm: interpolates outside image by size.",
+            "optional": true
+        },
+        {
+            "id": "pedir",
+            "name": "Pedir",
+            "type": "Number",
+            "integer": true,
+            "value-key": "[PEDIR]",
+            "command-line-flag": "-pedir",
+            "description": "An integer (int or long). Phase encode direction of epi - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z.",
+            "optional": true
+        },
+        {
+            "id": "ref_weight",
+            "name": "Ref weight",
+            "type": "File",
+            "value-key": "[REF_WEIGHT]",
+            "command-line-flag": "-refweight",
+            "description": "An existing file name. File for reference weighting volume.",
+            "optional": true
+        },
+        {
+            "id": "reference",
+            "name": "Reference",
+            "type": "File",
+            "value-key": "[REFERENCE]",
+            "command-line-flag": "-ref",
+            "description": "An existing file name. Reference file.",
+            "optional": false
+        },
+        {
+            "id": "rigid2D",
+            "name": "Rigid2d",
+            "type": "Flag",
+            "value-key": "[RIGID2D]",
+            "command-line-flag": "-2D",
+            "description": "A boolean. Use 2d rigid body mode - ignores dof.",
+            "optional": true
+        },
+        {
+            "id": "save_log",
+            "name": "Save log",
+            "type": "Flag",
+            "value-key": "[SAVE_LOG]",
+            "command-line-flag": "--save_log",
+            "description": "A boolean. Save to log file.",
+            "optional": true
+        },
+        {
+            "id": "schedule",
+            "name": "Schedule",
+            "type": "File",
+            "value-key": "[SCHEDULE]",
+            "command-line-flag": "-schedule",
+            "description": "An existing file name. Replaces default schedule.",
+            "optional": true
+        },
+        {
+            "id": "searchr_x",
+            "name": "Searchr x",
+            "type": "Number",
+            "list": true,
+            "integer": true,
+            "min-list-entries": 2,
+            "max-list-entries": 2,
+            "value-key": "[SEARCHR_X]",
+            "command-line-flag": "-searchrx",
+            "description": "A list of from 2 to 2 items which are an integer (int or long). Search angles along x-axis, in degrees.",
+            "optional": true
+        },
+        {
+            "id": "searchr_y",
+            "name": "Searchr y",
+            "type": "Number",
+            "list": true,
+            "integer": true,
+            "min-list-entries": 2,
+            "max-list-entries": 2,
+            "value-key": "[SEARCHR_Y]",
+            "command-line-flag": "-searchry",
+            "description": "A list of from 2 to 2 items which are an integer (int or long). Search angles along y-axis, in degrees.",
+            "optional": true
+        },
+        {
+            "id": "searchr_z",
+            "name": "Searchr z",
+            "type": "Number",
+            "list": true,
+            "integer": true,
+            "min-list-entries": 2,
+            "max-list-entries": 2,
+            "value-key": "[SEARCHR_Z]",
+            "command-line-flag": "-searchrz",
+            "description": "A list of from 2 to 2 items which are an integer (int or long). Search angles along z-axis, in degrees.",
+            "optional": true
+        },
+        {
+            "id": "sinc_width",
+            "name": "Sinc width",
+            "type": "Number",
+            "integer": true,
+            "value-key": "[SINC_WIDTH]",
+            "command-line-flag": "-sincwidth",
+            "description": "An integer (int or long). Full-width in voxels.",
+            "optional": true
+        },
+        {
+            "id": "sinc_window",
+            "name": "Sinc window",
+            "type": "String",
+            "value-key": "[SINC_WINDOW]",
+            "command-line-flag": "-sincwindow",
+            "description": "'rectangular' or 'hanning' or 'blackman'. Sinc window.",
+            "optional": true,
+            "value-choices": [
+                "rectangular",
+                "hanning",
+                "blackman"
+            ]
+        },
+        {
+            "id": "uses_qform",
+            "name": "Uses qform",
+            "type": "Flag",
+            "value-key": "[USES_QFORM]",
+            "command-line-flag": "-usesqform",
+            "description": "A boolean. Initialize using sform or qform.",
+            "optional": true
+        },
+        {
+            "id": "verbose",
+            "name": "Verbose",
+            "type": "Number",
+            "integer": true,
+            "value-key": "[VERBOSE]",
+            "command-line-flag": "-verbose",
+            "description": "An integer (int or long). Verbose mode, 0 is least.",
+            "optional": true
+        },
+        {
+            "id": "wm_seg",
+            "name": "Wm seg",
+            "type": "File",
+            "value-key": "[WM_SEG]",
+            "command-line-flag": "-wmseg",
+            "description": "A file name. White matter segmentation volume needed by bbr cost function.",
+            "optional": true
+        },
+        {
+            "id": "wmcoords",
+            "name": "Wmcoords",
+            "type": "File",
+            "value-key": "[WMCOORDS]",
+            "command-line-flag": "-wmcoords",
+            "description": "A file name. White matter boundary coordinates for bbr cost function.",
+            "optional": true
+        },
+        {
+            "id": "wmnorms",
+            "name": "Wmnorms",
+            "type": "File",
+            "value-key": "[WMNORMS]",
+            "command-line-flag": "-wmnorms",
+            "description": "A file name. White matter boundary normals for bbr cost function.",
+            "optional": true
+        }
+    ],
+    "output-files": [
+        {
+            "name": "Out file",
+            "id": "out_file",
+            "optional": true,
+            "description": "A file name. Registered output file.",
+            "path-template": "[IN_FILE]_flirt",
+            "value-key": "[OUT_FILE]",
+            "command-line-flag": "-out"
+        },
+        {
+            "name": "Out log",
+            "id": "out_log",
+            "optional": true,
+            "description": "A file name. Output log.",
+            "path-template": "[IN_FILE]_flirt.log",
+            "value-key": "[OUT_LOG]"
+        },
+        {
+            "name": "Out matrix file",
+            "id": "out_matrix_file",
+            "optional": true,
+            "description": "A file name. Output affine matrix in 4x4 asciii format.",
+            "path-template": "[IN_FILE]_flirt.mat",
+            "value-key": "[OUT_MATRIX_FILE]",
+            "command-line-flag": "-omat"
+        },
+        {
+            "name": "Out file",
+            "id": "out_file",
+            "path-template": "out_file",
+            "optional": true,
+            "description": "An existing file name. Path/name of registered file (if generated)."
+        },
+        {
+            "name": "Out log",
+            "id": "out_log",
+            "path-template": "out_log",
+            "optional": true,
+            "description": "A file name. Path/name of output log (if generated)."
+        },
+        {
+            "name": "Out matrix file",
+            "id": "out_matrix_file",
+            "path-template": "out_matrix_file",
+            "optional": true,
+            "description": "An existing file name. Path/name of calculated affine transform (if generated)."
+        }
+    ],
+    "groups": [
+        {
+            "id": "all_or_none_group",
+            "name": "All or none group",
+            "members": [
+                "save_log",
+                "out_log"
+            ],
+            "all-or-none": true
+        },
+        {
+            "id": "mutex_group",
+            "name": "Mutex group",
+            "members": [
+                "apply_isoxfm",
+                "apply_xfm"
+            ],
+            "mutually-exclusive": true
+        }
+    ],
+    "tool-version": "1.0.0",
+    "schema-version": "0.5",
+    "container-image": {
+        "image": "mcin/docker-fsl:latest",
+        "type": "docker",
+        "index": "index.docker.io"
+    },
+    "tags": {
+        "domain": "neuroinformatics",
+        "source": "nipype-interface"
+    }
+}
\ No newline at end of file
diff --git a/nipype/utils/tests/test_nipype2boutiques.py b/nipype/utils/tests/test_nipype2boutiques.py
index 926de0f2cd..f5c6c6494a 100644
--- a/nipype/utils/tests/test_nipype2boutiques.py
+++ b/nipype/utils/tests/test_nipype2boutiques.py
@@ -2,16 +2,40 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 from future import standard_library
-standard_library.install_aliases()
-
 from ..nipype2boutiques import generate_boutiques_descriptor
+import json
+standard_library.install_aliases()
 
 
 def test_generate():
-    generate_boutiques_descriptor(module='nipype.interfaces.ants.registration',
-                                  interface_name='ANTS',
-                                  container_image=None,
-                                  container_index=None,
-                                  container_type=None,
-                                  verbose=False,
-                                  save=False)
+    ignored_inputs = [
+        "args",
+        "environ",
+        "output_type"
+    ]
+    desc = generate_boutiques_descriptor(module='nipype.interfaces.fsl',
+                                         interface_name='FLIRT',
+                                         container_image=('mcin/'
+                                                          'docker-fsl:latest'),
+                                         container_index='index.docker.io',
+                                         container_type='docker',
+                                         verbose=False,
+                                         save=False,
+                                         ignore_inputs=ignored_inputs,
+                                         author=("Oxford Centre for Functional"
+                                                 " MRI of the Brain (FMRIB)"))
+
+    with open('nipype/utils/nipype2boutiques_example.json', 'r',
+              encoding='utf-8') as desc_file:
+        assert ordered(json.loads(desc)) == ordered(json.load(desc_file))
+
+
+# Recursively sorts all items in a JSON object
+# Used when comparing two JSON objects whose ordering may differ
+def ordered(obj):
+    if isinstance(obj, dict):
+        return sorted((k, ordered(v)) for k, v in obj.items())
+    if isinstance(obj, list):
+        return sorted(ordered(x) for x in obj)
+    else:
+        return obj

From 2ff50eda8cf09914867ad72212e064735216600e Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Thu, 28 Mar 2019 21:55:58 -0400
Subject: [PATCH 23/28] fix test file path

---
 nipype/utils/tests/test_nipype2boutiques.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/utils/tests/test_nipype2boutiques.py b/nipype/utils/tests/test_nipype2boutiques.py
index f5c6c6494a..520f3c7862 100644
--- a/nipype/utils/tests/test_nipype2boutiques.py
+++ b/nipype/utils/tests/test_nipype2boutiques.py
@@ -25,7 +25,7 @@ def test_generate():
                                          author=("Oxford Centre for Functional"
                                                  " MRI of the Brain (FMRIB)"))
 
-    with open('nipype/utils/nipype2boutiques_example.json', 'r',
+    with open('utils/nipype2boutiques_example.json', 'r',
               encoding='utf-8') as desc_file:
         assert ordered(json.loads(desc)) == ordered(json.load(desc_file))
 

From c828feca0efe3108736e0869da33689082897b4c Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Fri, 29 Mar 2019 16:46:24 -0400
Subject: [PATCH 24/28] fixed test

---
 nipype/{utils => testing/data}/nipype2boutiques_example.json | 0
 nipype/utils/tests/test_nipype2boutiques.py                  | 4 ++--
 2 files changed, 2 insertions(+), 2 deletions(-)
 rename nipype/{utils => testing/data}/nipype2boutiques_example.json (100%)

diff --git a/nipype/utils/nipype2boutiques_example.json b/nipype/testing/data/nipype2boutiques_example.json
similarity index 100%
rename from nipype/utils/nipype2boutiques_example.json
rename to nipype/testing/data/nipype2boutiques_example.json
diff --git a/nipype/utils/tests/test_nipype2boutiques.py b/nipype/utils/tests/test_nipype2boutiques.py
index 520f3c7862..f3ad944650 100644
--- a/nipype/utils/tests/test_nipype2boutiques.py
+++ b/nipype/utils/tests/test_nipype2boutiques.py
@@ -3,6 +3,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 from future import standard_library
 from ..nipype2boutiques import generate_boutiques_descriptor
+from nipype.testing import example_data
 import json
 standard_library.install_aliases()
 
@@ -25,8 +26,7 @@ def test_generate():
                                          author=("Oxford Centre for Functional"
                                                  " MRI of the Brain (FMRIB)"))
 
-    with open('utils/nipype2boutiques_example.json', 'r',
-              encoding='utf-8') as desc_file:
+    with open(example_data('nipype2boutiques_example.json'), 'r') as desc_file:
         assert ordered(json.loads(desc)) == ordered(json.load(desc_file))
 
 

From 7e96311e26f8589e980576a1b6f13fcd9796a51d Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Tue, 2 Apr 2019 10:33:05 -0400
Subject: [PATCH 25/28] changed test to only check a subset of descriptor
 fields

---
 nipype/utils/tests/test_nipype2boutiques.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/nipype/utils/tests/test_nipype2boutiques.py b/nipype/utils/tests/test_nipype2boutiques.py
index f3ad944650..5bba16be6f 100644
--- a/nipype/utils/tests/test_nipype2boutiques.py
+++ b/nipype/utils/tests/test_nipype2boutiques.py
@@ -27,7 +27,21 @@ def test_generate():
                                                  " MRI of the Brain (FMRIB)"))
 
     with open(example_data('nipype2boutiques_example.json'), 'r') as desc_file:
-        assert ordered(json.loads(desc)) == ordered(json.load(desc_file))
+        # Make sure that output descriptor matches the expected descriptor.
+        output_desc = json.loads(desc)
+        expected_desc = json.load(desc_file)
+        assert (output_desc.get('name') ==
+                expected_desc.get('name'))
+        assert (output_desc.get('author') ==
+                expected_desc.get('author'))
+        assert (output_desc.get('command-line') ==
+                expected_desc.get('command-line'))
+        assert (output_desc.get('description') ==
+                expected_desc.get('description'))
+        assert (ordered(output_desc.get('inputs')) ==
+                ordered(expected_desc.get('inputs')))
+        assert (ordered(output_desc.get('container-image')) ==
+                ordered(expected_desc.get('container-image')))
 
 
 # Recursively sorts all items in a JSON object

From 0eae216930657d07f80ee02b0a0e1dd93e93cd00 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Thu, 4 Apr 2019 14:53:37 -0400
Subject: [PATCH 26/28] changed test again

---
 nipype/utils/tests/test_nipype2boutiques.py | 21 ++++++---------------
 1 file changed, 6 insertions(+), 15 deletions(-)

diff --git a/nipype/utils/tests/test_nipype2boutiques.py b/nipype/utils/tests/test_nipype2boutiques.py
index 5bba16be6f..19735df6b5 100644
--- a/nipype/utils/tests/test_nipype2boutiques.py
+++ b/nipype/utils/tests/test_nipype2boutiques.py
@@ -38,18 +38,9 @@ def test_generate():
                 expected_desc.get('command-line'))
         assert (output_desc.get('description') ==
                 expected_desc.get('description'))
-        assert (ordered(output_desc.get('inputs')) ==
-                ordered(expected_desc.get('inputs')))
-        assert (ordered(output_desc.get('container-image')) ==
-                ordered(expected_desc.get('container-image')))
-
-
-# Recursively sorts all items in a JSON object
-# Used when comparing two JSON objects whose ordering may differ
-def ordered(obj):
-    if isinstance(obj, dict):
-        return sorted((k, ordered(v)) for k, v in obj.items())
-    if isinstance(obj, list):
-        return sorted(ordered(x) for x in obj)
-    else:
-        return obj
+        assert (len(output_desc.get('inputs')) ==
+                len(expected_desc.get('inputs')))
+        assert(len(output_desc.get('output-files')) ==
+               len(expected_desc.get('output-files')))
+        assert (output_desc.get('container-image').get('image') ==
+                expected_desc.get('container-image').get('image'))

From 52d87a9cf091668f292ad57c77fcce28ce4b33af Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Tue, 9 Apr 2019 22:33:18 -0400
Subject: [PATCH 27/28] added handling for lists with value choices, fixed
 logic to handle case when command line flag includes a 0 or 1 (seen in FNIRT)

---
 nipype/utils/nipype2boutiques.py | 38 ++++++++++++++++++--------------
 1 file changed, 22 insertions(+), 16 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index a9500a71a8..5f88239da1 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -268,15 +268,7 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose,
     elif handler_type == "Float":
         inp['type'] = "Number"
     elif handler_type == "Bool":
-        if (spec.argstr and len(spec.argstr.split("=")) > 1 and
-                (spec.argstr.split("=")[1] == '0'
-                 or spec.argstr.split("=")[1] == '1')):
-            inp['type'] = "Number"
-            inp['integer'] = True
-            inp['minimum'] = 0
-            inp['maximum'] = 1
-        else:
-            inp['type'] = "Flag"
+        inp['type'] = "Flag"
     else:
         inp['type'] = "String"
 
@@ -296,14 +288,24 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose,
     # TODO handle lists of lists (e.g. FSL ProbTrackX seed input)
     if handler_type == "List":
         inp['list'] = True
-        trait_type = type(trait_handler.item_trait.trait_type).__name__
-        if trait_type == "Int":
+        item_type = trait_handler.item_trait.trait_type
+        item_type_name = type(item_type).__name__
+        if item_type_name == "Int":
             inp['integer'] = True
             inp['type'] = "Number"
-        elif trait_type == "Float":
+        elif item_type_name == "Float":
             inp['type'] = "Number"
-        elif trait_type == "File":
+        elif item_type_name == "File":
             inp['type'] = "File"
+        elif item_type_name == "Enum":
+            value_choices = item_type.values
+            if value_choices is not None:
+                if all(isinstance(n, int) for n in value_choices):
+                    inp['type'] = "Number"
+                    inp['integer'] = True
+                elif all(isinstance(n, float) for n in value_choices):
+                    inp['type'] = "Number"
+                inp['value-choices'] = value_choices
         else:
             inp['type'] = "String"
         if trait_handler.minlen != 0:
@@ -532,7 +534,7 @@ def generate_custom_inputs(desc_inputs):
     for desc_input in desc_inputs:
         if desc_input['type'] == 'Flag':
             custom_input_dicts.append({desc_input['id']: True})
-        elif desc_input.get('value-choices'):
+        elif desc_input.get('value-choices') and not desc_input.get('list'):
             for value in desc_input['value-choices']:
                 custom_input_dicts.append({desc_input['id']: value})
     return custom_input_dicts
@@ -578,8 +580,12 @@ def get_command_line_flag(input_spec, is_flag_type=False, input_name=None):
     flag, flag_sep = None, None
     if input_spec.argstr:
         if "=" in input_spec.argstr:
-            flag = input_spec.argstr.split("=")[0].strip()
-            flag_sep = "="
+            if (input_spec.argstr.split("=")[1] == '0'
+                    or input_spec.argstr.split("=")[1] == '1'):
+                flag = input_spec.argstr
+            else:
+                flag = input_spec.argstr.split("=")[0].strip()
+                flag_sep = "="
         elif input_spec.argstr.split("%")[0]:
             flag = input_spec.argstr.split("%")[0].strip()
     elif is_flag_type:

From 5c0684d77c712ed115376b2884cdaa956b5539d1 Mon Sep 17 00:00:00 2001
From: Erin Benderoff <erin.benderoff@gmail.com>
Date: Wed, 24 Apr 2019 16:47:12 -0400
Subject: [PATCH 28/28] removed six, changed all-or-none groups to go under
 requires-inputs field instead

---
 nipype/utils/nipype2boutiques.py | 23 ++++++-----------------
 1 file changed, 6 insertions(+), 17 deletions(-)

diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py
index 5f88239da1..4f692a267b 100644
--- a/nipype/utils/nipype2boutiques.py
+++ b/nipype/utils/nipype2boutiques.py
@@ -19,7 +19,6 @@
 import os
 import sys
 import simplejson as json
-import six
 
 from ..scripts.instance import import_module
 
@@ -310,7 +309,7 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose,
             inp['type'] = "String"
         if trait_handler.minlen != 0:
             inp['min-list-entries'] = trait_handler.minlen
-        if trait_handler.maxlen != six.MAXSIZE:
+        if trait_handler.maxlen != sys.maxsize:
             inp['max-list-entries'] = trait_handler.maxlen
         if spec.sep:
             inp['list-separator'] = spec.sep
@@ -353,6 +352,8 @@ def get_boutiques_input(inputs, interface, input_name, spec, verbose,
         inp['optional'] = False
     if spec.usedefault:
         inp['default-value'] = spec.default_value()[1]
+    if spec.requires is not None:
+        inp['requires-inputs'] = spec.requires
 
     try:
         value_choices = trait_handler.values
@@ -422,7 +423,8 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs):
 
     # Handle multi-outputs
     if (isinstance(output_value, list) or
-            type(spec.handler).__name__ == "OutputMultiObject"):
+            type(spec.handler).__name__ == "OutputMultiObject" or
+            type(spec.handler).__name__ == "List"):
         output['list'] = True
         if output_value:
             # Check if all extensions are the same
@@ -451,32 +453,19 @@ def get_boutiques_output(outputs, name, spec, interface, tool_inputs):
 def get_boutiques_groups(input_traits):
     """
     Returns a list of dictionaries containing Boutiques groups for the mutually
-    exclusive and all-or-none Nipype inputs.
+    exclusive Nipype inputs.
     """
     desc_groups = []
-    all_or_none_input_sets = []
     mutex_input_sets = []
 
     # Get all the groups
     for name, spec in input_traits:
-        if spec.requires is not None:
-            group_members = set([name] + list(spec.requires))
-            if group_members not in all_or_none_input_sets:
-                all_or_none_input_sets.append(group_members)
         if spec.xor is not None:
             group_members = set([name] + list(spec.xor))
             if group_members not in mutex_input_sets:
                 mutex_input_sets.append(group_members)
 
     # Create a dictionary for each one
-    for i, inp_set in enumerate(all_or_none_input_sets, 1):
-        desc_groups.append({'id': "all_or_none_group" +
-                                  ("_" + str(i) if i != 1 else ""),
-                            'name': "All or none group" +
-                                    (" " + str(i) if i != 1 else ""),
-                            'members': list(inp_set),
-                            'all-or-none': True})
-
     for i, inp_set in enumerate(mutex_input_sets, 1):
         desc_groups.append({'id': "mutex_group" +
                                   ("_" + str(i) if i != 1 else ""),