Wrap for shp2msh and msh2vtu

tools/msh2vtu.xml

@@ -0,0 +1,103 @@
+<tool id="msh2vtu" name="GMSH_To_VTU_Converter" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+    <description>
+        Convert GMSH mesh files to VTU format using various options for mesh processing.
+    </description>
+    <requirements>
+        <requirement type="package" version="3.6">python</requirement>
+        <requirement type="package" version="0.5">meshio</requirement>
+        <requirement type="package" version="0.1">numpy</requirement>
+        <requirement type="package" version="0.1">ogs</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_file' input_file.msh &&
+        msh2vtu input_file.msh 
+            -p '$prefix' 
+            -d '$dim' 
+            #if $delz == "true"
+                -z
+            #end if
+            #if $swapxy == "true"
+                -s
+            #end if
+            #if $reindex == "true"
+                -r
+            #end if
+            #if $keep_ids == "true"
+                -k
+            #end if
+            #if $ascii == "true"
+                -a
+            #end if
+            -l '$log_level'
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="GMSH" label="Input GMSH File"/>
+        <param name="prefix" type="text" label="Filename Prefix" argument="-p">
+            <validator type="regex">^(?!.*[\u003C\u003E])[a-zA-Z0-9_]+$</validator>
+        </param>
+        <param name="dim" type="select" label="Mesh Dimension" argument="-d">
+            <option value="1">1</option>
+            <option value="2">2</option>
+            <option value="3">3</option>
+        </param>
+        <param name="delz" type="boolean" value="false" label="Delete Z Coordinate" optional="true" argument="-z"/>
+        <param name="swapxy" type="boolean" value="false" label="Swap XY Coordinates" optional="true" argument="-s"/>
+        <param name="reindex" type="boolean" value="false" label="Reindex" optional="true" argument="-r"/>
+        <param name="keep_ids" type="boolean" value="false" label="Keep IDs" optional="true" argument="-k"/>
+        <param name="ascii" type="boolean" value="false" label="ASCII Output" optional="true" argument="-a"/>
+        <param name="log_level" type="select" value="DEBUG" label="Log Level" argument="-l">
+            <option value="DEBUG">DEBUG</option>
+            <option value="INFO">INFO</option>
+            <option value="WARNING">WARNING</option>
+            <option value="ERROR">ERROR</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_data" format="vtu" label="Output vtu file" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" value="/home/stehling/.venv/lib/python3.10/site-packages/ogstools/msh2vtu/test-data/geolayers_2d.msh"/>
+            <param name="prefix" value="test"/>
+            <param name="dim" value="3"/>
+            <param name="delz" value="False"/>
+            <param name="swapxy" value="False"/>
+            <param name="reindex" value="False"/>
+            <param name="keep_ids" value="False"/>
+            <param name="ascii" value="True"/>
+            <param name="log_level" value="DEBUG"/>
+            <output name="output_data" file="test_output.vtu"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+    **Overview:**
+
+This Galaxy tool converts GMSH mesh files (`*.msh`) into VTU format (`*.vtu`) using the OpenGeoSys (OGS) utility. The tool offers several options for mesh processing, such as deleting the Z coordinate, swapping XY coordinates, reindexing nodes, and keeping original IDs.
+
+**Inputs:**
+
+1. **Input GMSH File:** The GMSH mesh file to be converted.
+2. **Output Path:** (Optional) Specify the output path where the VTU file will be saved. If not specified, the current working directory is used.
+3. **Filename Prefix:** Prefix to be added to the output filename.
+4. **Mesh Dimension (dim):** Select the desired mesh dimension (0, 1, 2, or 3). Default is `0`.
+5. **Delete Z Coordinate (delz):** Boolean flag to remove the Z coordinate from the mesh. Set to `True` to enable.
+6. **Swap XY Coordinates (swapxy):** Boolean flag to swap the X and Y coordinates. Set to `True` to enable.
+7. **Reindex:** Boolean flag to reindex the nodes. Set to `True` to enable.
+8. **Keep IDs:** Boolean flag to keep the original node and cell IDs. Set to `True` to enable.
+9. **ASCII Output:** Boolean flag to output the file in ASCII format instead of binary. Set to `True` to enable.
+10. **Log Level:** Set the level of logging details (DEBUG, INFO, WARNING, ERROR). Default is `DEBUG`.
+
+**Outputs:**
+
+- **Output VTU File:** The converted mesh file in VTU format.
+
+**Usage Notes:**
+
+- This tool requires that the input file is in GMSH format (`*.msh`).
+- The resulting output will be a VTU file (`*.vtu`) that can be used with visualization tools and other software supporting the VTU format.
+- The output directory must be writable; otherwise, the tool will fail to save the output file.
+    ]]></help>
+<citations> 
+    <citation type="doi">10.5281/zenodo.13685289</citation>
+</citations>
+</tool>

tools/ogs_tools/.shed.yml

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+name: suite_ogs_tools
+owner: ufz
+description: Convert GMSH mesh files to VTU format using various options for mesh processing.
+long_description: |
+    This Galaxy tool converts GMSH mesh files (`*.msh`) into VTU format (`*.vtu`) using the OpenGeoSys (OGS) utility. 
+    The tool offers several options for mesh processing, such as deleting the Z coordinate, swapping XY coordinates, reindexing nodes, and keeping original IDs.
+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: "Wrapper for bankfull discharge calculation function: {{ tool_name }}."
+suite:
+  name: suite_ogs_tools
+  description: Convert GMSH mesh files to VTU format using various options for mesh processing.
+  long_description: |
+    This Galaxy tool converts GMSH mesh files (`*.msh`) into VTU format (`*.vtu`) using the OpenGeoSys (OGS) utility. 
+    The tool offers several options for mesh processing, such as deleting the Z coordinate, swapping XY coordinates, reindexing nodes, and keeping original IDs.

tools/ogs_tools/shp2msh.xml

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+<tool id="shp2msh" name="shp2msh_converter" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
+    <requirements>
+        <requirement type="package" version="0.0.3">ogstools</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        export SHAPE_RESTORE_SHX=YES &&    
+        ln -s '$input_shp' input.shp &&
+        cat input.shx > /home/stehling/ogs_tools/content_of_input.txt &&
+        shp2msh --input input.shp --output output.vtu
+        #if str($cellsize)!="":
+            --cellsize '$cellsize'
+        #end if
+        '$meshing'
+        '$simplify'
+    ]]></command>
+    <inputs>
+        <param name="input_shp" type="data" format="shp" label="shp input data" 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" label="output_data"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_shp" value="/home/stehling/ogs_tools/test-data/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>
+    </tests>
+    <help><![CDATA[
+        This tool takes a shapefile 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.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.5281/zenodo.13685289</citation>
+    </citations>
+</tool>