Wrap for shp2msh and msh2vtu

tools/ogstools/Converter/.shed.yml

@@ -0,0 +1,18 @@
+name: suite_ogs_tools
+owner: ufz
+description: A suite of tools for OpenGeoSys (ogs)
+long_description: |
+     A suite of tools for ogs.
+categories:
+- Ecology
+remote_repository_url: https://gitlab.opengeosys.org/ogs/tools/ogstools
+homepage_url: https://www.opengeosys.org/
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: A suite of tools for OpenGeoSys (ogs)
+suite:
+  name: suite_ogs_tools
+  description: A suite of tools for ogs.
+  long_description: |
+      A suite of tools for ogs.

tools/ogstools/Converter/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">0.4.0</token>
+    <token name="@PROFILE@">23.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+
+    <xml name="ogs_requirement">
+            <requirement type="package" version="@TOOL_VERSION@">ogstools</requirement>
+            <yield/>
+
+    </xml>
+
+    <xml name="ogs_citation">
+        <citations> 
+            <citation type="doi">10.5281/zenodo.13685289</citation>
+        </citations>
+    </xml>
+
+    <xml name="creator">
+        <creator>
+            <organization name="Helmholtz Centre for Environmental Research - UFZ" url ="https://www.ufz.de/"/>
+        </creator>
+    </xml>
+</macros>

tools/ogstools/Converter/msh2vtu.xml

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+
+<tool id="msh2vtu" name="ogstools msh2vtu" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Convert msh to UnstructuredGrid (vtk)
+    </description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <expand macro="creator"/>
+    <requirements>
+        <expand macro="ogs_requirement"/>
+    </requirements>      
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' input_file.msh &&
+        msh2vtu input_file.msh 
+            -d '$dim' 
+            $delz $swapxy $reindex $keep_ids $ascii
+            -l '$log_level'
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="GMSH" label="Input GMSH File"/>
+        <param name="dim" type="select" label="Set dimensionality of the mesh" argument="-d">
+            <option value="1">1D</option>
+            <option value="2">2D</option>
+            <option value="3">3D</option>
+        </param>
+        <param name="delz" type="boolean" value="false" truevalue="-z" falsevalue="" label="Delete Z Coordinate" optional="true" argument="-z"/>
+        <param name="swapxy" type="boolean" value="false" truevalue="-s" falsevalue="" label="Swap XY Coordinates" optional="true" argument="-s"/>
+        <param name="reindex" type="boolean" value="false" truevalue="-r" falsevalue="" label="Reindex" optional="true" argument="-r"/>
+        <param name="keep_ids" type="boolean" value="false" truevalue="-k" falsevalue="" label="Keep IDs" optional="true" argument="-k"/>
+        <param name="ascii" type="boolean" value="false" truevalue="-a" falsevalue="" label="ASCII Output" optional="true" argument="-a"/>
+        <param name="log_level" type="select" label="Log Level" argument="-l">
+            <option value="ERROR" selected="true">ERROR</option>
+            <option value="DEBUG">DEBUG</option>
+            <option value="INFO">INFO</option>
+            <option value="WARNING">WARNING</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="boundary" format="xml" label="${tool.name}: boundary" from_work_dir="input_file_boundary.vtu" />
+        <data name="domain" format="xml" label="${tool.name}: domain" from_work_dir="input_file_domain.vtu" />
+        <data name="physical_group_Bottom" format="xml" label="${tool.name}: physical_group_Bottom" from_work_dir="input_file_physical_group_Bottom.vtu" />
+        <data name="physical_group_Left" format="xml" label="${tool.name}: physical_group_Left" from_work_dir="input_file_physical_group_Left.vtu" />
+        <data name="physical_group_Right" format="xml" label="${tool.name}: physical_group_Right" from_work_dir="input_file_physical_group_Right.vtu" />
+        <data name="physical_group_RockBed" format="xml" label="${tool.name}: physical_group_RockBed" from_work_dir="input_file_physical_group_RockBed.vtu" />
+        <data name="physical_group_SedimentLayer1" format="xml" label="${tool.name}: physical_group_SedimentLayer1" from_work_dir="input_file_physical_group_SedimentLayer1.vtu" />
+        <data name="physical_group_SedimentLayer2" format="xml" label="${tool.name}: physical_group_SedimentLayer2" from_work_dir="input_file_physical_group_SedimentLayer2.vtu" />
+        <data name="physical_group_SedimentLayer3" format="xml" label="${tool.name}: physical_group_SedimentLayer3" from_work_dir="input_file_physical_group_SedimentLayer3.vtu" />
+        <data name="physical_group_Top" format="xml" label="${tool.name}: physical_group_Top" from_work_dir="input_file_physical_group_Top.vtu" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="geolayers_2d.msh"/>
+            <param name="dim" value="2"/>
+            <param name="delz" value="True"/>
+            <param name="swapxy" value="True"/>
+            <param name="reindex" value="True"/>
+            <param name="keep_ids" value="True"/>
+            <param name="ascii" value="True"/>
+            <param name="log_level" value="DEBUG"/>
+            <output name="boundary" file="input_file_boundary.vtu"/>
+            <output name="domain" file="input_file_domain.vtu"/>
+            <output name="physical_group_Bottom" file="input_file_physical_group_Bottom.vtu"/>
+            <output name="physical_group_Left" file="input_file_physical_group_Left.vtu"/>
+            <output name="physical_group_Right" file="input_file_physical_group_Right.vtu"/>
+            <output name="physical_group_RockBed" file="input_file_physical_group_RockBed.vtu"/>
+            <output name="physical_group_SedimentLayer1" file="input_file_physical_group_SedimentLayer1.vtu"/>
+            <output name="physical_group_SedimentLayer2" file="input_file_physical_group_SedimentLayer2.vtu"/>
+            <output name="physical_group_SedimentLayer3" file="input_file_physical_group_SedimentLayer3.vtu"/>
+            <output name="physical_group_Top" file="input_file_physical_group_Top.vtu"/> 
+        </test>
+    </tests>
+    <help><![CDATA[
+    **Overview:**
+
+        msh2vtu is a application that converts a Gmsh (.msh) file for use in OGS by extracting domain-, boundary- and physical group-submeshes and saves them in a set of files in the vtu format.
+        Supported element types:
+        - lines (linear and quadratic) in 1D
+        - triangles and quadrilaterals (linear and quadratic) in 2D
+        - tetra- and hexahedrons (linear and quadratic) in 3D
+
+    **Inputs:**
+
+        1. **Input GMSH File:** The GMSH (.msh) file to be converted.
+        2. **Mesh Dimension (dim):** Select the desired mesh dimension (1, 2, or 3).
+        3. **Delete Z Coordinate (delz):** Boolean flag to remove the Z coordinate from the mesh (for 2D meshes with z=0).
+        4. **Swap XY Coordinates (swapxy):** Boolean flag to swap the X and Y coordinates.
+        5. **Reindex (reindex):** Renumber physical group / region / Material IDs to be renumbered beginning with zero.
+        6. **Keep IDs (keep_ids):** By default, rename gmsh:physical to MaterialIDs and change type of corresponding cell data to INT32. If True, this is skipped.
+        7. **ASCII Output (ascii):** Boolean flag to output the file in ASCII format instead of binary.
+        8. **Log Level (log_level):** Set the level of logging details (DEBUG, INFO, WARNING, ERROR).
+
+    **Outputs:**
+
+        **Output VTU Files:** The converted mesh file as a set of files with VTU format.
+    ]]></help>
+    <expand macro="ogs_citation"/>
+</tool>

tools/ogstools/Converter/shp2msh.xml

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+<tool id="shp2msh" name="ogstools shp2msh" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Convert shp to msh
+    </description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <expand macro="creator"/>
+    <requirements>
+        <expand macro="ogs_requirement"/>
+    </requirements>  
+    <command detect_errors="exit_code"><![CDATA[
+        export SHAPE_RESTORE_SHX=YES &&    
+        ln -s '$input_shp' input.shp &&
+        shp2msh --input input.shp --output output.vtu
+        #if str($cellsize)!="":
+            --cellsize '$cellsize'
+        #end if
+        '$meshing'
+        '$simplify'
+    ]]></command>
+    <inputs>
+        <param name="input_shp" type="data" format="shp" label="Input SHP File" argument="-i"/>
+        <param name="cellsize" type="float" min="40" optional="true" label="cellsize" argument="-c"/>
+        <param name="meshing" type="select"  label="meshing">
+            <option value="triangle" selected="true">Triangle</option>
+            <option value="gmsh">Gmsh</option>
+        </param>
+        <param name="simplify" type="select" label="simplify">
+            <option value="simplified">Simplified</option>
+            <option value="original" selected="true">Original</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="xml" from_work_dir="output.vtu"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_shp" value="circle.shp"/>
+            <param name="cellsize" value="500.0"/>
+            <param name="meshing" value= "triangle"/>
+            <param name="simplify" value="simplified"/>
+            <output name="output" value="output.vtu"/>
+        </test>
+        <test>
+            <param name="input_shp" value="circle.shp"/>
+            <param name="meshing" value= "gmsh"/>
+            <param name="simplify" value="original"/>
+            <output name="output" value="output2.vtu"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **Overview:**
+            This tool takes a shapefile (.shp) as input and creates a mesh using either the Triangle or GMSH method.
+            The cellsize can be optionally specified, and the shapefile can be simplified before meshing.
+            Output data has the format .vtu/ .vtk.
+
+        **Inputs:**
+
+            1. **Input Shape File:** The .shp file to be converted.
+            2. **Cellsize:** Select the desired cellsize min=40.
+            3. **Meshing:** Choose either triangle or gmsh.
+            4. **Simplify:** Either the shapefiles are kept unchanged or they can be simplified. Choose between original and simplified.
+
+        **Outputs:**
+
+            **Output VTU Files:** The converted mesh as a VTU file.
+    ]]></help>
+    <expand macro="ogs_citation"/>
+</tool>