Ogs add layer generate mesh

tools/ogs/.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 ogs

tools/ogs/addLayer.xml

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+<tool id="ogs_addlayer" name="OGS AddLayer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Adds a layer to an existing mesh
+    </description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <expand macro="ogs_requirement"/>
+    </requirements> 
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$input_mesh' input.vtu &&
+        AddLayer -i input.vtu -o output.vtu -t '$layer_thickness'
+        $add_layer_on_bottom
+        #if str($material_option.material_id) == "copy":
+            $copy_material_ids
+        #end if    
+        #if str($material_option.material_id) == "set":
+            --set-material-id $material_option.set_material_id
+        #end if
+
+    ]]></command>
+    <inputs> 
+        <param name="input_mesh" type="data" format="vtkxml" label="Input Mesh File" argument="-i"/>
+        <param name="layer_thickness" type="float" label="Layer Thickness" argument="-t"/>
+        <param name="add_layer_on_bottom" type="boolean" value="false" truevalue="--add-layer-on-bottom" falsevalue="" label="Add Layer To Bottom"/>
+         <conditional name="material_option">
+            <param name="material_id" type="select" label="Material ID Option">
+                <option value="none" selected="true">None</option>
+                <option value="copy">Copy existing material IDs</option>
+                <option value="set">Set a specific material ID</option>
+            </param>
+            <when value="none">
+            </when>
+            <when value="copy">
+                <param name="copy_material_ids" type="boolean" truevalue="--copy-material-ids" falsevalue="" label="Copy/Save Material IDs"/>
+            </when>
+            <when value="set">
+                <param name="set_material_id" type="integer" label="Set Material IDs"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_mesh" format="vtkxml" label="Output Mesh File" from_work_dir="output.vtu" />
+    </outputs>
+    <tests>
+    <test>
+        <param name="input_mesh" value="tm_a_quad.vtu"/>
+        <param name="layer_thickness" value="15.0"/>
+        <param name="add_layer_on_bottom" value="false"/>
+        <param name="material_option|material_id" value="set"/>
+        <param name="material_option|set_material_id" value="1"/>
+        <output name="output_mesh" value="tm_a_quad_with_extra_layer.vtu"/>
+    </test>
+</tests>
+    <help><![CDATA[
+        **Overview:**
+
+            This Galaxy tool adds a new layer to an existing mesh using the OpenGeoSys library. It processes meshes in the VTU (Visualization Toolkit Unstructured Grid) format.
+
+        **Inputs:**
+
+            1. **Input Mesh File (`input_mesh`)**  The VTU file containing the existing mesh to which a new layer will be added.  
+            2. **Layer Thickness (`layer_thickness`)**  Specifies the thickness of the new layer to be added. The default value is `10.0`.  
+            3. **Add Layer to Bottom (`add_layer_on_bottom`)**  If selected, the layer is added to the bottom of the mesh. Otherwise, it is added to the top.  
+            4. **Material ID Option (`material_option`)**  Determines how material IDs for the new layer are managed:  
+                - `None`: No material ID modifications are applied.  
+                - `Copy`: Copies existing material IDs to the new layer.  
+                - `Set`: Sets a specific material ID for the new layer.  
+
+        **Outputs:**
+
+1.          **Output Mesh File (`output_mesh`)**  The resulting mesh file in VTU format with the added layer.  
+    ]]></help>
+    <expand macro="ogs_citation"/>
+</tool>

tools/ogs/generateStructuredMesh.xml

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+<tool id="ogs_generatestructuredmesh" name="OGS GenerateStructuredMesh" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>
+        Generation of simple meshes
+    </description>
+    <macros>
+        <import>macros.xml</import>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <expand macro="ogs_requirement"/>
+    </requirements>
+    <expand macro="creator"/>
+    <command detect_errors="exit_code"><![CDATA[
+    generateStructuredMesh 
+        -o output.$output_ext
+        -e $element_type
+    #if str($length_x) != "":
+        --lx $length_x
+    #end if
+    #if str($length_y) != "":
+        --ly $length_y
+    #end if
+    #if str($length_z) != "":
+        --lz $length_z
+    #end if
+    #if str($subdiv_x) != "":
+        --nx $subdiv_x
+    #end if
+    #if str($subdiv_y) != "":
+        --ny $subdiv_y
+    #end if
+    #if str($subdiv_z) != "":
+        --nz $subdiv_z
+    #end if
+    #if str($element_length_x) != "":
+        --dx0 $element_length_x
+    #end if
+    #if str($element_length_y) != "":
+        --dy0 $element_length_y
+    #end if
+    #if str($element_length_z) != "":
+        --dz0 $element_length_z
+    #end if
+    #if str($max_element_length_x) != "":
+        --dx-max $max_element_length_x
+    #end if
+    #if str($max_element_length_y) != "":
+        --dy-max $max_element_length_y
+    #end if
+    #if str($max_element_length_z) != "":
+        --dz-max $max_element_length_z
+    #end if
+    #if str($multiplier_x) != "":
+        --mx $multiplier_x
+    #end if
+    #if str($multiplier_y) != "":
+        --my $multiplier_y
+    #end if
+    #if str($multiplier_z) != "":
+        --mz $multiplier_z
+    #end if
+    && mv output.$output_ext '$output'
+
+    ]]></command>
+    <inputs>
+        <param name="output_ext" type="select" label="Output File Format" argument="-o">
+            <option value="vtu">VTK Unstructured Grid</option>
+            <option value="msh">GMSH</option>
+        </param>
+        <param name="element_type" type="select" label="Element Type" argument="-e">
+            <option value="line">Line</option>
+            <option value="tri">Triangle</option>
+            <option value="quad">Quadrilateral</option>
+            <option value="hex">Hexahedron</option>
+            <option value="prism">Prism</option>
+            <option value="tet">Tetrahedron</option>
+            <option value="pyramid">Pyramid</option>
+        </param>      
+        <param name="length_x" type="float" min="0" optional="true" label="Length in X" help="Length of the domain in the X direction.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="length_y" type="float" min="0" optional="true" label="Length in Y" help="Length of the domain in the Y direction.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="length_z" type="float" min="0" optional="true" label="Length in Z" help="Length of the domain in the Z direction.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="subdiv_x" type="integer" min="1" optional="true" label="Subdivisions in X" help="Number of subdivisions in the X direction. Overrides element length argument."/>
+        <param name="subdiv_y" type="integer" min="1" optional="true" label="Subdivisions in Y" help="Number of subdivisions in the Y direction. Overrides element length argument."/>
+        <param name="subdiv_z" type="integer" min="1" optional="true" label="Subdivisions in Z" help="Number of subdivisions in the Z direction. Overrides element length argument."/>
+        <param name="element_length_x" type="float" min="0" optional="true" label="Initial Element Length X" help="Initial element length in the X direction. If the value of this parameter is smaller than subdivions or maximum length parameters it gets overridden.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="element_length_y" type="float" min="0" optional="true" label="Initial Element Length Y" help="Initial element length in the Y direction. If the value of this parameter is smaller than subdivions or maximum length parameters it gets overridden.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="element_length_z" type="float" min="0" optional="true" label="Initial Element Length Z" help="Initial element length in the Z direction. If the value of this parameter is smaller than subdivions or maximum length parameters it gets overridden.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="max_element_length_x" type="float" min="0" optional="true" label="Maximum Element Length X" help="Maximum element length in the X direction. Overrides element length argument.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="max_element_length_y" type="float" min="0" optional="true" label="Maximum Element Length Y" help="Maximum element length in the Y direction. Overrides element length argument.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="max_element_length_z" type="float" min="0" optional="true" label="Maximum Element Length Z" help="Maximum element length in the Z direction. Overrides element length argument.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="multiplier_x" type="float" min="0" optional="true" label="Multiplier X" help="Multiplier for element lengths in the X direction.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="multiplier_y" type="float" min="0" optional="true" label="Multiplier Y" help="Multiplier for element lengths in the Y direction.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+        <param name="multiplier_z" type="float" min="0" optional="true" label="Multiplier Z" help="Multiplier for element lengths in the Z direction.">
+            <validator type="in_range" min="0" exclude_min="true"/>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="vtkxml" name="output" label="Format: ${output_ext}">
+            <change_format>
+                <when input="output_ext" value="msh" format="gmsh.msh"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="output_ext" value="vtu"/>
+            <param name="element_type" value="quad"/>
+            <param name="length_x" value="3"/>
+            <param name="length_y" value="4"/>
+            <output name="output" value="quad_3x4.vtu" ftype="vtkxml"/>
+        </test>
+        <test>
+            <param name="output_ext" value="msh"/>
+            <param name="element_type" value="hex"/>
+            <param name="length_x" value="4"/>
+            <param name="length_y" value="5"/>
+            <param name="length_z" value="6"/>
+            <param name="multiplier_x" value="0.8"/>
+            <param name="multiplier_y" value="1.1"/>
+            <param name="multiplier_z" value="2"/>
+            <param name="max_element_length_z" value="1"/>
+            <param name="element_length_y" value="0.1"/>
+            <param name="element_length_z" value="0.1"/>
+            <output name="output" value="hex_4x5x6.msh"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+    **Overview:**
+        This tool generates structured meshes using the OpenGeoSys Mesh Generator. 
+        Users can define the element type, dimensions, subdivisions, and other parameters to create a customized mesh.
+        Output data is written in the specified format (VTU/ VTK Unstructured Grid or GMSH).
+
+    **Inputs:**
+        1. **Output Format:** The format of the output file (.vtu or .msh) 
+        2. **Element Type:** The type of element to create (e.g., line, triangle, quadrilateral, etc.).
+        3. **Length (X, Y, Z):** The length of the mesh domain in the X, Y, and Z directions.
+        4. **Subdivisions (X, Y, Z):** Number of subdivisions in each direction to define mesh resolution.
+        5. **Initial Element Length (X, Y, Z):** Initial size of the elements in the X, Y, and Z directions.
+        6. **Maximum Element Length (X, Y, Z):** Maximum size of elements for gradual refinement.
+        7. **Multiplier (X, Y, Z):** Refinement multiplier for element lengths in each direction.
+
+    **Outputs:**
+
+        **Output Mesh File:** The generated structured mesh saved as a file in the specified format.
+    ]]></help>
+    <expand macro="ogs_citation"/>
+</tool>

tools/ogs/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">6.5.3</token>
+    <token name="@PROFILE@">23.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+
+    <xml name="ogs_requirement">
+            <requirement type="package" version="@TOOL_VERSION@">ogs</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>