annotate pcdl_get_substrate_list.xml @ 0:d769482946e0 draft default tip

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

<tool id="pcdl_get_substrate_list" name="pcdl_get_substrate_list" 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_get_substrate_list 'output_pc'
        --verbose $verbose
        > '$substrate_txt'
    ]]></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>
        <data name="substrate_txt" label="substrate_txt" format="txt"/>
    </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="true"/>
            </section>
            <output name="substrate_txt">
                <assert_contents>
                    <has_text text="['"/>
                    <has_text text="']"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
This function is returns all chemical species names, modeled in the microenvironment, ordered by subsrate ID.

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