SaQC wrapper with GUI

tools/saqc/.shed.yml

@@ -0,0 +1,9 @@
+categories:
+- Statistics
+description:  System for automated Quality Control
+long_description: Anomalies and errors are the rule not the exception when working with time series data. This is especially true, if such data originates from in-situ measurements of environmental properties. Almost all applications, however, implicily rely on data, that complies with some definition of 'correct'. In order to infer reliable data products and tools, there is no alternative to quality control. SaQC provides all the building blocks to comfortably bridge the gap between 'usually faulty' and 'expected to be corrected' in a accessible, consistent, objective and reproducible way.
+name: saqc
+owner: mbernt
+remote_repository_url: https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/
+homepage_url: https://git.ufz.de/rdm-software/saqc
+type: unrestricted

tools/saqc/TODO.md

@@ -0,0 +1,8 @@
+saqc:
+
+- module docstrings missing (except for breaks)
+- flagPatternByDTW missing type annotation
+- missing `--version` CLI argument
+- allow tsv for `--config`
+- list[x] should be List[X]? some parameters (eg field) are inconsistently annotated as Sequence/list
+

tools/saqc/example.py

@@ -0,0 +1,152 @@
+#!/usr/bin/env python
+import galaxyxml.tool as gxt
+import galaxyxml.tool.parameters as gxtp
+
+tool = gxt.Tool(
+    "aragorn",
+    "se.lu.mbioekol.mbio-serv2.aragorn",
+    "1.2.36",
+    "Aragorn is a tRNA finder",
+    "aragorn.exe",
+    version_command="aragorn.exe --version",
+)
+
+inputs = gxtp.Inputs()
+outputs = gxtp.Outputs()
+
+# Add requirements
+requirements = gxtp.Requirements()
+requirements.append(gxtp.Requirement("package", "samtools", version="1.0.0"))
+requirements.append(gxtp.Container("docker", "one_super_image"))
+tool.requirements = requirements
+
+# A parameter
+param = gxtp.BooleanParam("flag", label="Flag label", help="Flag help", num_dashes=1)
+# Yes I know this is rubbish. Please make a PR!!
+param.space_between_arg = " "
+inputs.append(param)
+
+
+# A float in a section
+section = gxtp.Section("float_section", "Float section")
+param = gxtp.FloatParam(
+    "float", value=0, label="Float label", help="Float help", num_dashes=1
+)
+param.space_between_arg = " "
+section.append(param)
+param = gxtp.FloatParam(
+    None, argument="--float-fromarg", value=0, label="Float label", help="Float help"
+)
+section.append(param)
+inputs.append(section)
+
+# A conditional
+param = gxtp.Conditional("cond", label="Conditional")
+param.append(gxtp.SelectParam("Select", options={"hi": "1", "bye": "2"}))
+when_a = gxtp.When(value="hi")
+when_b = gxtp.When(value="bye")
+when_b.append(
+    gxtp.IntegerParam("some_int", value=0, num_dashes=1, label="Advanced value")
+)
+param.append(when_a)
+param.append(when_b)
+inputs.append(param)
+
+# Integer parameters
+param_min = gxtp.IntegerParam(
+    "int_min", label="int_min label", help="int_min help", value=0, num_dashes=1
+)
+param_max = gxtp.IntegerParam(
+    "int_max", label="int_max label", help="int_max help", value=0, num_dashes=1
+)
+
+posint = gxtp.IntegerParam(
+    "posint",
+    label="posint label",
+    positional=True,
+    help="posinthelp",
+    value=0,
+    num_dashes=2,
+)
+
+param_min.command_line_override = "-i$int_min,$int_max"
+param_max.command_line_override = ""
+param_min.space_between_arg = " "
+param_max.space_between_arg = " "
+inputs.append(param_min)
+inputs.append(param_max)
+inputs.append(posint)
+
+# Add Select with options from_file with columns and filter
+param = gxtp.SelectParam("select_local")
+options = gxtp.Options(from_file="loc_file.loc")
+column_a = gxtp.Column("name", 0)
+options.append(column_a)
+column_b = gxtp.Column("value", 1)
+options.append(column_b)
+filter_a = gxtp.Filter("sort_by", name="sorted", column="1")
+options.append(filter_a)
+param.append(options)
+inputs.append(param)
+
+param = gxtp.Repeat("repeat", "repeat title")
+data = gxtp.DataParam(
+    "data",
+    argument="--data",
+    optional=True,
+    format="fasta",
+    multiple=True,
+    label="data label",
+    help="data help",
+)
+param.append(data)
+inputs.append(param)
+
+# Configfiles
+configfiles = gxtp.Configfiles()
+configfiles.append(gxtp.Configfile(name="testing", text="Hello <> World"))
+configfiles.append(gxtp.ConfigfileDefaultInputs(name="inputs"))
+
+# Outputs
+param = gxtp.OutputData("output", format="tabular", num_dashes=1)
+param.space_between_arg = " "
+outputs.append(param)
+# Collection
+collection = gxtp.OutputCollection("supercollection", label="a small label")
+discover = gxtp.DiscoverDatasets(r"(?P&lt;designation&gt;.+)\.pdf.fasta", format="fasta")
+collection.append(discover)
+outputs.append(collection)
+
+tool.inputs = inputs
+tool.outputs = outputs
+tool.help = "HI"
+tool.configfiles = configfiles
+
+# Add Tests sections
+tool.tests = gxtp.Tests()
+test_a = gxtp.Test()
+param = gxtp.TestParam("float", value=5.4)
+test_a.append(param)
+test_out = gxtp.TestOutput(name="output", value="file.out")
+test_a.append(test_out)
+coll_out = gxtp.TestOutputCollection(name="pdf_out")
+test_a.append(coll_out)
+rep_out = gxtp.TestRepeat(name="testrepeat")
+param = gxtp.TestParam("repeatchild", value="foo")
+rep_out.append(param)
+test_a.append(rep_out)
+test_coll = gxtp.TestOutputCollection(name="pdf_out")
+test_elem = gxtp.TestOCElement(name="apdf", file="apdf", ftype="pdf")
+test_coll.append(test_elem)
+test_a.append(test_coll)
+rep_out = gxtp.TestRepeat(name="output_repeat")
+param = gxtp.TestOutput(name="repeatout", value="repeatfile.out")
+rep_out.append(param)
+test_a.append(rep_out)
+tool.tests.append(test_a)
+
+
+# Add comment to the wrapper
+tool.add_comment("This tool descriptor has been generated using galaxyxml.")
+
+print(tool.export())