mergeMSP.xml

<tool id="mergemsp" name="Merge MSP Spectra" version="0.1.0" python_template_version="3.5">
   <creator>
        <person
            givenName="Wudmir"
            familyName="Rojas"
            url="https://github.com/wverastegui"
            identifier="0000-0001-7036-9987" />
        <person
            givenName="Helge"
            familyName="Hecht"
            url="https://github.com/hechth"
            identifier="0000-0001-6744-996X" />
        <organization
            url="https://www.recetox.muni.cz/"
            email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
            name="RECETOX MUNI"/>
    </creator>
    <description>Merge MSP Spectra files</description>
    <requirements>
         <requirement type="package" version="0.14.0">matchms</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
       #set newinput = str("' '").join([str($f) for $f in $input])
        python3  $__tool_directory__/mergeMSP.py
        --filenames    '$newinput'
        --outfilename  '$outfile'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="msp" multiple="true"/>
    </inputs>
    <outputs>
        <data name="outfile" format="msp" />
    </outputs>
    <tests>
         <test>
            <param name="input">
              <collection type="paired">
                <element name="input" value="1-NITROPYRENE.msp"/>
                <element name="input" value="2,3-DICHLOROPHENOL.msp"/>
                <element name="input" value="2,4-DICHLOROPHENOL.msp"/>
              </collection>
            </param>
            <output name="outfile" file="sample_output.msp" ftype="msp" />
        </test>
    </tests> 
    <help><![CDATA[
        Mergemsp handles input/output files in MSP format using the matchms.importing and matchms.exporting modules (https://matchms.readthedocs.io/en/latest/index.html).
    ]]></help>
</tool>