Ogs auto wrap

tools/ogsAutowrap/.shed.yml

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+name: suite_ogs
+owner: ufz
+description: A suite of tools for OpenGeoSys (ogs)
+long_description: A suite of tools for ogs
+categories:
+- Geo Science
+remote_repository_url: https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs/
+homepage_url: https://gitlab.opengeosys.org/ogs/ogs
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: A suite of tools for OpenGeoSys (ogs)
+suite:
+  name: suite_ogs
+  description: A suite of tools for ogs
+  long_description: A suite of tools for og

tools/ogsAutowrap/AddElementQuality.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: AddElementQuality" id="ogs_addelementquality" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'AddElementQuality'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[AddElementQuality --version]]></version_command>
+  <command><![CDATA[
+ln -sf '$input_mesh_file' '$input_mesh_file.element_identifier';
+AddElementQuality
+    --quality_criterion '$quality_criterion'
+    --input_mesh_file '$input_mesh_file.element_identifier'
+    --output_mesh_file output_1.vtu
+]]></command>
+  <inputs>
+    <param argument="--quality_criterion" type="select" optional="true" label="quality criterion" help="quality criterion" multiple="false">
+      <option value="ElementSize">ElementSize</option>
+      <option value="EdgeRatio">EdgeRatio</option>
+      <option value="EquiAngleSkew">EquiAngleSkew</option>
+      <option value="RadiusEdgeRatio">RadiusEdgeRatio</option>
+      <option value="SizeDifference">SizeDifference</option>
+    </param>
+    <param argument="--input_mesh_file" type="data" optional="false" label="input mesh file" help="Input (.vtu | .msh) mesh file" format="vtkxml" />
+  </inputs>
+  <outputs>
+    <data name="output_AddElementQuality" format="vtkxml" label="Output from AddElementQuality" from_work_dir="output_1.vtu" hidden="false" />
+  </outputs>
+  <tests>
+    <expand macro="addelementquality_test" />
+  </tests>
+  <help>This tool runs the **AddElementQuality** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>

tools/ogsAutowrap/AddFaultToVoxelGrid.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: AddFaultToVoxelGrid" id="ogs_addfaulttovoxelgrid" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'AddFaultToVoxelGrid'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[AddFaultToVoxelGrid --version]]></version_command>
+  <command><![CDATA[
+ln -sf '$fault' '$fault.element_identifier';
+ln -sf '$input' '$input.element_identifier';
+AddFaultToVoxelGrid
+    --fault '$fault.element_identifier'
+    --input '$input.element_identifier'
+    --output output_1.vtu
+]]></command>
+  <inputs>
+    <param argument="--fault" type="data" optional="false" label="fault" help="Input (.vtu). Name of mesh file representing fault" format="vtkxml" />
+    <param argument="--input" type="data" optional="false" label="input" help="Input (.vtu). Name of the input file containing the paths the all input in correct order from top to bottom" format="vtkxml" />
+  </inputs>
+  <outputs>
+    <data name="output_AddFaultToVoxelGrid" format="vtkxml" label="Output from AddFaultToVoxelGrid" from_work_dir="output_1.vtu" hidden="false" />
+  </outputs>
+  <tests>
+    <expand macro="addfaulttovoxelgrid_test" />
+  </tests>
+  <help>This tool runs the **AddFaultToVoxelGrid** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>

tools/ogsAutowrap/AddLayer.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: AddLayer" id="ogs_addlayer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'AddLayer'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[AddLayer --version]]></version_command>
+  <command><![CDATA[
+ln -sf '$input_mesh_file' '$input_mesh_file.element_identifier';
+AddLayer
+    --input-mesh-file '$input_mesh_file.element_identifier'
+    --layer-tickness '$layer_tickness'
+    $add_layer_on_bottom
+    $copy_material_ids
+    --set-material-id '$set_material_id'
+    --output-mesh-file output_1.vtu
+]]></command>
+  <inputs>
+    <param argument="--input-mesh-file" type="data" optional="false" label="input mesh file" help="Input (.vtu). The name of the file containing the mesh" format="vtkxml" />
+    <param argument="--layer-tickness" type="float" optional="true" label="layer tickness" help="the thickness of the new layer, (min = 0)" />
+    <param argument="--add-layer-on-bottom" type="boolean" label="add layer on bottom" help="Per default the layer is add on the top, if this argument is set the layer is add on the bottom." checked="false" truevalue="--add-layer-on-bottom" falsevalue="" />
+    <param argument="--copy-material-ids" type="boolean" label="copy material ids" help="Copy the existing material distribution of the layer which is to be extended. If the switch isn't given a new material id will be created." checked="false" truevalue="--copy-material-ids" falsevalue="" />
+    <param argument="--set-material-id" type="integer" optional="true" label="set material id" help="the material id of the new layer, (min = 0)" />
+  </inputs>
+  <outputs>
+    <data name="output_AddLayer" format="vtkxml" label="Output from AddLayer" from_work_dir="output_1.vtu" hidden="false" />
+  </outputs>
+  <tests>
+    <expand macro="addlayer_test" />
+  </tests>
+  <help>This tool runs the **AddLayer** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>

tools/ogsAutowrap/AssignRasterDataToMesh.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: AssignRasterDataToMesh" id="ogs_assignrasterdatatomesh" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'AssignRasterDataToMesh'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[AssignRasterDataToMesh --version]]></version_command>
+  <command><![CDATA[
+ln -sf '$raster' '$raster.element_identifier';
+ln -sf '$input' '$input.element_identifier';
+AssignRasterDataToMesh
+    --nodata '$nodata'
+    $cell_array
+    $node_array
+    --scalar-name '$scalar_name'
+    --raster '$raster.element_identifier'
+    --input '$input.element_identifier'
+    --output output_1.vtu
+]]></command>
+  <inputs>
+    <param argument="--nodata" type="float" optional="true" label="nodata" help="The no data value used for missing values (min = 0)" />
+    <param argument="--cell-array" type="boolean" label="cell array" help="Assigns raster data to cell array" checked="false" truevalue="--cell-array" falsevalue="" />
+    <param argument="--node-array" type="boolean" label="node array" help="Assigns raster data to node array (default)" checked="false" truevalue="--node-array" falsevalue="" />
+    <param argument="--scalar-name" type="text" optional="true" label="scalar name" help="The name of the newly created scalar array." />
+    <param argument="--raster" type="data" optional="false" label="raster" help="Input (.asc). Name of the input raster file" format="raster.asc" />
+    <param argument="--input" type="data" optional="false" label="input" help="Input (.vtu). Name of the input mesh file" format="vtkxml" />
+  </inputs>
+  <outputs>
+    <data name="output_AssignRasterDataToMesh" format="vtkxml" label="Output from AssignRasterDataToMesh" from_work_dir="output_1.vtu" hidden="false" />
+  </outputs>
+  <tests>
+    <expand macro="assignrasterdatatomesh_test" />
+  </tests>
+  <help>This tool runs the **AssignRasterDataToMesh** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>

tools/ogsAutowrap/ComputeNodeAreasFromSurfaceMesh.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: ComputeNodeAreasFromSurfaceMesh" id="ogs_computenodeareasfromsurfacemesh" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'ComputeNodeAreasFromSurfaceMesh'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[ComputeNodeAreasFromSurfaceMesh --version]]></version_command>
+  <command><![CDATA[
+ln -sf '$mesh_input_file' '$mesh_input_file.element_identifier';
+ComputeNodeAreasFromSurfaceMesh
+    --mesh-input-file '$mesh_input_file.element_identifier'
+    --id-prop-name '$id_prop_name'
+    --output-base-name 'new_'
+]]></command>
+  <inputs>
+    <param argument="--mesh-input-file" type="data" optional="false" label="mesh input file" help="Input (.vtu). The name of the file containing the input mesh" format="vtkxml" />
+    <param argument="--id-prop-name" type="select" optional="true" label="id prop name" help="the name of the property containing the id information" multiple="false">
+      <option value="bulk_node_ids">bulk_node_ids</option>
+      <option value="bulk_element_ids">bulk_element_ids</option>
+      <option value="bulk_edge_ids">bulk_edge_ids</option>
+      <option value="bulk_face_ids">bulk_face_ids</option>
+    </param>
+  </inputs>
+  <outputs>
+    <collection name="tool_outputs" type="list" label="Outputs from ComputeNodeAreasFromSurfaceMesh">
+      <discover_datasets pattern="(?P&lt;designation&gt;new_.*)" format="csv" visible="true" />
+    </collection>
+  </outputs>
+  <tests>
+    <expand macro="computenodeareasfromsurfacemesh_test" />
+  </tests>
+  <help>This tool runs the **ComputeNodeAreasFromSurfaceMesh** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>

tools/ogsAutowrap/CreateAnchors.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: CreateAnchors" id="ogs_createanchors" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'CreateAnchors'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[CreateAnchors --version]]></version_command>
+  <command><![CDATA[
+CreateAnchors
+    --output output_1.vtu
+]]></command>
+  <inputs />
+  <outputs>
+    <data name="output_CreateAnchors" format="vtkxml" label="Output from CreateAnchors" from_work_dir="output_1.vtu" hidden="false" />
+  </outputs>
+  <tests>
+    <expand macro="createanchors_test" />
+  </tests>
+  <help>This tool runs the **CreateAnchors** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>

tools/ogsAutowrap/CreateBoundaryConditionsAlongPolylines.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: CreateBoundaryConditionsAlongPolylines" id="ogs_createboundaryconditionsalongpolylines" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'CreateBoundaryConditionsAlongPolylines'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[CreateBoundaryConditionsAlongPolylines --version]]></version_command>
+  <command><![CDATA[
+ln -sf '$input_geometry' '$input_geometry.element_identifier';
+ln -sf '$mesh_file' '$mesh_file.element_identifier';
+ln -sf '$gmsh_path' '$gmsh_path.element_identifier';
+CreateBoundaryConditionsAlongPolylines
+    $gml
+    --type '$type'
+    --input-geometry '$input_geometry.element_identifier'
+    --mesh-file '$mesh_file.element_identifier'
+    --gmsh-path '$gmsh_path.element_identifier'
+    --output-base-file-name 'new_'
+]]></command>
+  <inputs>
+    <param argument="--gml" type="boolean" label="gml" help="Write found nodes to gml file." checked="false" truevalue="--gml" falsevalue="" />
+    <param argument="--type" type="select" optional="true" label="type" help="the process type the boundary condition will be written for currently LIQUID_FLOW (primary variable PRESSURE1) and GROUNDWATER_FLOW (primary variable HEAD, default) are supported," multiple="false">
+      <option value="LIQUID_FLOW">LIQUID_FLOW</option>
+      <option value="GROUNDWATER_FLOW">GROUNDWATER_FLOW</option>
+    </param>
+    <param argument="--input-geometry" type="data" optional="false" label="input geometry" help="Input (.gml | .gli). The name of the input file containing the geometry" format="xml" />
+    <param argument="--mesh-file" type="data" optional="false" label="mesh file" help="Input (.vtu). The name of the input file containing the mesh" format="vtkxml" />
+    <param argument="--gmsh-path" type="data" optional="true" label="gmsh path" help="Input (.msh). The path to the gmsh binary" format="msh" />
+  </inputs>
+  <outputs>
+    <collection name="tool_outputs" type="list" label="Outputs from CreateBoundaryConditionsAlongPolylines">
+      <discover_datasets pattern="(?P&lt;designation&gt;new_.*)" format="geometry (gli" visible="true" />
+    </collection>
+  </outputs>
+  <tests>
+    <expand macro="createboundaryconditionsalongpolylines_test" />
+  </tests>
+  <help>This tool runs the **CreateBoundaryConditionsAlongPolylines** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>

tools/ogsAutowrap/ExtractBoundary.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: ExtractBoundary" id="ogs_extractboundary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'ExtractBoundary'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[ExtractBoundary --version]]></version_command>
+  <command><![CDATA[
+ln -sf '$mesh_input_file' '$mesh_input_file.element_identifier';
+ExtractBoundary
+    --mesh-input-file '$mesh_input_file.element_identifier'
+    $ascii_output
+    --mesh-output-file output_1.vtu
+]]></command>
+  <inputs>
+    <param argument="--mesh-input-file" type="data" optional="false" label="mesh input file" help="Input (.vtu). The name of the file containing the input mesh" format="vtkxml" />
+    <param argument="--ascii-output" type="boolean" label="ascii output" help="If the switch is set use ascii instead of binary format for data in the vtu output." checked="false" truevalue="--ascii-output" falsevalue="" />
+  </inputs>
+  <outputs>
+    <data name="output_ExtractBoundary" format="vtkxml" label="Output from ExtractBoundary" from_work_dir="output_1.vtu" hidden="false" />
+  </outputs>
+  <tests>
+    <expand macro="extractboundary_test" />
+  </tests>
+  <help>This tool runs the **ExtractBoundary** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>

tools/ogsAutowrap/ExtractMaterials.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: ExtractMaterials" id="ogs_extractmaterials" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'ExtractMaterials'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[ExtractMaterials --version]]></version_command>
+  <command><![CDATA[
+ln -sf '$input' '$input.element_identifier';
+ExtractMaterials
+    --material-id '$material_id'
+    --input '$input.element_identifier'
+    --output output_1.vtu
+]]></command>
+  <inputs>
+    <param argument="--material-id" type="integer" optional="true" label="material id" help="The MaterialID for which elements should be extracted into a new mesh." />
+    <param argument="--input" type="data" optional="false" label="input" help="Input (.vtu). Name of the input mesh" format="vtkxml" />
+  </inputs>
+  <outputs>
+    <data name="output_ExtractMaterials" format="vtkxml" label="Output from ExtractMaterials" from_work_dir="output_1.vtu" hidden="false" />
+  </outputs>
+  <tests>
+    <expand macro="extractmaterials_test" />
+  </tests>
+  <help>This tool runs the **ExtractMaterials** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>

tools/ogsAutowrap/ExtractSurface.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: ExtractSurface" id="ogs_extractsurface" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'ExtractSurface'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[ExtractSurface --version]]></version_command>
+  <command><![CDATA[
+ln -sf '$mesh_input_file' '$mesh_input_file.element_identifier';
+ExtractSurface
+    $ascii_output
+    --angle '$angle'
+    --y-component '$y_component'
+    --x-component '$x_component'
+    --mesh-input-file '$mesh_input_file.element_identifier'
+    --mesh-output-file output_1.vtu
+]]></command>
+  <inputs>
+    <param argument="--ascii-output" type="boolean" label="ascii output" help="If the switch is set use ascii instead of binary format for data in the vtu output." checked="false" truevalue="--ascii-output" falsevalue="" />
+    <param argument="--angle" type="float" optional="true" label="angle" help="tolerated angle (in degrees) between given normal and element normal, (min = 0), (max = 360)" />
+    <param argument="--y-component" type="float" optional="true" label="y component" help="y component of the normal" />
+    <param argument="--x-component" type="float" optional="true" label="x component" help="x component of the normal" />
+    <param argument="--mesh-input-file" type="data" optional="false" label="mesh input file" help="Input (.vtu). The name of the file containing the input mesh" format="vtkxml" />
+  </inputs>
+  <outputs>
+    <data name="output_ExtractSurface" format="vtkxml" label="Output from ExtractSurface" from_work_dir="output_1.vtu" hidden="false" />
+  </outputs>
+  <tests>
+    <expand macro="extractsurface_test" />
+  </tests>
+  <help>This tool runs the **ExtractSurface** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>

tools/ogsAutowrap/FEFLOW2OGS.xml

@@ -0,0 +1,27 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool name="OGS: FEFLOW2OGS" id="ogs_feflow2ogs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01">
+  <description>Galaxy wrapper for the OGS utility 'FEFLOW2OGS'.</description>
+  <macros>
+    <import>macros.xml</import>
+    <import>test_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <version_command><![CDATA[feflow2ogs --version]]></version_command>
+  <command><![CDATA[
+ln -sf '$in' '$in.element_identifier';
+feflow2ogs
+    --in '$in.element_identifier'
+    --out output_1.if extension is msh, old OGS file format is written
+]]></command>
+  <inputs>
+    <param argument="--in" type="data" optional="false" label="in" help="Input (.fem). FEFLOW input file" format="feflow.fem" />
+  </inputs>
+  <outputs>
+    <data name="output_FEFLOW2OGS" format="if extension is msh, old ogs file format is written" label="Output from FEFLOW2OGS" from_work_dir="output_1.if extension is msh, old OGS file format is written" hidden="false" />
+  </outputs>
+  <tests>
+    <expand macro="feflow2ogs_test" />
+  </tests>
+  <help>This tool runs the **FEFLOW2OGS** utility from the OpenGeoSys suite.</help>
+  <expand macro="citations" />
+</tool>