annotate addLayer.xml @ 2:3e3794ac4fab draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs/ commit 4444a06cda0781c444fade827201712e34633c29

<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>
    <expand macro="creator"/>
    <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
        #elif 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" value="" 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">Leave as it is</option>
                <option value="copy">Copy existing material IDs</option>
                <option value="set">Set a specific material ID</option>
            </param>
            <when value="none"/>
            <when value="copy"/>
            <when value="set">
                <param name="set_material_id" type="integer" value="" label="Set Material IDs"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_mesh" format="vtkxml" 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:
                - `Copy`: Copies existing material IDs to the new layer.  
                - `Set`: Sets a specific material ID for the new layer.  

        **Outputs:**

            **Output Mesh File (`output_mesh`)**  The resulting mesh file in VTU format with the added layer.  
    ]]></help>
    <expand macro="ogs_citation"/>
</tool>