view dma-filelist-generation.xml @ 2:21d2cd76bb1b draft

planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty

<tool id="dma_filelist_generation" name="dma_filelist_generation" version="0.1.0">
    <description>Generate filelist for DMA DIMS nearline</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="python"><![CDATA[
        dma-filelist-generation.py
        -i
        #for $i  in  $library
            $__app__.config.user_library_import_dir/$__user_email__/$i.library
        #end for
        -o .
        #if $check_mzml
            --check_mzml
        #end if
        #if $check_raw
            --check_raw
        #end if
        #if $create_filelist_mzml
            --create_filelist_mzml
        #end if
        #if $create_filelist_raw
            --create_filelist_raw
        #end if

    ]]></command>

    <inputs>

        <repeat name="library" title="Library directories containing *.mzml or *.raw files"
                    help="multiple directories can be used to make one filelist, for cases where
                           the files for different classes are in different directories">
            <param name="library" type="text" size="40" >
                    <validator type="empty_field" />
            </param>
        </repeat>

        <param name="check_mzml" checked="true" type="boolean" label="Check mzML files?" help=""/>
        <param name="check_raw" checked="true" type="boolean" label="Check raw files?" help=""/>
        <param name="create_filelist_mzml" type="boolean" label="Create filelist for mzML files?" help=""/>
        <param name="create_filelist_raw" checked="true" type="boolean" label="Create filelist for raw files?" help=""/>


    </inputs>
    <outputs>
        <data name="filelist_mzml" label="${tool.name} on ${on_string}: filelist mzML"
              from_work_dir="filelist_mzml.tsv" format="tsv">
            <filter>create_filelist_mzml is True</filter>
        </data>
        <data name="filelist_raw" label="${tool.name} on ${on_string}: filelist raw"
              from_work_dir="filelist_raw.tsv" format="tsv">
            <filter>create_filelist_raw is True</filter>
        </data>

    </outputs>
    <tests>

    </tests>
    <help><![CDATA[


    ]]></help>
</tool>