view pcdl_make_conc_vtk.xml @ 0:0f6d33a7b252 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16

<tool id="pcdl_make_conc_vtk" name="pcdl_make_conc_vtk" version="3.0.1+galaxy0" profile="21.05">
    <macros>
        <import>pcdl_macros.xml</import>
    </macros>
    <requirements>
        <expand macro="requirement"/>
    </requirements>
    <command><![CDATA[
        #import re
        mkdir output_pc &&
        #for $file in $path:
            #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
            ln -s '$file' output_pc/$filename &&
        #end for

        pcdl_make_conc_vtk 'output_pc'
        --verbose $verbose
    ]]></command>
    <inputs>
        <section name="essential" title="essential:" expanded="true">
            <expand macro="path"/>
        </section>
        <section name="advanced" title="advanced:" expanded="false">
            <expand macro="verbose"/>
        </section>
    </inputs>
    <outputs>
        <collection name="conc_vtk" type="list">
            <discover_datasets pattern="(?P&lt;designation&gt;.+_conc\.vtr)" format="vtkxml" directory="output_pc" visible="false"/>
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <section name="essential">
                <param name="path">
                    <expand macro="output"/>
                </param>
            </section>
            <section name="advanced">
                <param name="verbose" value="false"/>
            </section>
            <output_collection name="conc_vtk" count="2">
                <element name="output00000000_conc.vtr">
                    <assert_contents>
                        <has_text text="VTKFile type=&quot;RectilinearGrid&quot;"/>
                        <has_text text="RectilinearGrid"/>
                        <has_text text="VTKFile&gt;"/>
                    </assert_contents>
                </element>
                <element name="output00000001_conc.vtr">
                    <assert_contents>
                        <has_text text="VTKFile type=&quot;RectilinearGrid&quot;"/>
                        <has_text text="RectilinearGrid"/>
                        <has_text text="VTKFile&gt;"/>
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Function generates rectilinear grid vtk files, one per mcds time step, contains distribution of substrates over microenvironment. You can post-process this files in other software like paraview (https://www.paraview.org/).

Homepage: https://github.com/elmbeech/physicelldataloader
    ]]></help>
    <citations>
        <expand macro="citation"/>
    </citations>
</tool>