annotate extractSurface.xml @ 0:3dea3e30e6fc draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/ogs/ commit 8d522c2d14b28a4df096a5a13cd800bbf086f09f

<tool id="ogs_extractsurface" name="OGS extractSurface" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>
        Extracts a 2D surface from a 3D 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 &&
        ExtractSurface -i input.vtu -o outputExtracted2D.vtu
        -x $x_component -y $y_component -z $z_component 
        #if $angle:
            -a $angle 
        #end if
        $ascii_output
        
    ]]></command>
    <inputs>
        <param name="input_mesh" type="data" format="vtkxml" label="Input Mesh" help="3D input mesh in VTU format"/>
        <param name="x_component" type="float" label="X Component of Normal" help="X component of the normal vector"/>
        <param name="y_component" type="float" label="Y Component of Normal" help="Y component of the normal vector"/>
        <param name="z_component" type="float" label="Z Component of Normal" help="Z component of the normal vector"/>
        <param name="angle" type="float" label="Angle" optional="true" min="0" max="360" help="Tolerated angle between given normal and element normal (in degrees)"/>
        <param name="ascii_output" type="boolean" value="false" optional="true" truevalue="--ascii-output" falsevalue="" label="ASCII Output" help="Output VTU in ASCII format instead of binary"/>
    </inputs>
    <outputs>
        <data name="output_mesh" format="vtkxml" from_work_dir="outputExtracted2D.vtu"/>
    </outputs>
    <tests>
        <test>
            <param name="input_mesh" value="cube_1x1x1_hex_1e3_layers_10.vtu"/>
            <param name="x_component" value="0.0"/>
            <param name="y_component" value="0.0"/>
            <param name="z_component" value="1.0"/>
            <param name="angle" value="45.0"/>
            <param name="ascii_output" value="true"/>
            <output name="output_mesh" value="outputExtracted2D.vtu"/>
        </test>
    </tests>
    <help><![CDATA[
    **Overview:**
        This tool extracts 2D surface elements from a 3D mesh file. The surface is defined by specifying a normal vector and an angle of tolerance. The tool supports input and output in VTU or MSH formats and offers an option to save results in ASCII format for human readability.
    
    **Inputs:**
        1. **Input Mesh:** The 3D mesh file (in VTU or MSH format) from which the surface will be extracted.
        2. **Normal Vector Components:**
           - **X Component (-x):** X-component of the surface normal vector. Default is `0.0`.
           - **Y Component (-y):** Y-component of the surface normal vector. Default is `0.0`.
           - **Z Component (-z):** Z-component of the surface normal vector. Default is `-1.0`.
        3. **Angle (-a):** Tolerated angle (in degrees) between the given normal vector and the surface element normals. Default is `90.0`.
        4. **ASCII Output (--ascii-output):** A flag to save the output mesh in human-readable ASCII format instead of the default binary format.
    
    **Outputs:**
         **Extracted Surface Mesh:** The 2D surface mesh saved in VTU format, containing original IDs for nodes, elements, and faces. These IDs are useful for boundary conditions or source terms in simulations.
    
    ]]></help>
    <expand macro="ogs_citation"/>
</tool>