comparison temp.xml @ 18:e198b686bfe4 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit edf843bf10fa262f075980626a9201078f868757

17:e7d3dc3e0ec9

<tool id ="run_TEMP" name="TEMP" version="0.2.0">
    <description></description>
    <requirements>
        <!-- The following are classical toolshed packages and should be removed
        once conda is deemed stable-->
        <requirement type="package" version="1.6.922">bioperl</requirement>

        -s $__tool_directory__/scripts
        -r "$te_locations"
        -t "$reference2bit"
        -f "$median_insertsize"
        -c \${GALAXY_SLOTS:-2} &&
        zip archive.zip  *insertion* *excision* *absence* && mv archive.zip $archive &&
        mv alignment.insertion.refined.bp.summary $insertion_summary &&
        mv alignment.absence.refined.bp.summary $absence_summary
    ]]></command>
    <inputs>
        <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
        <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>
        <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/>

        <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum difference between mapping scores"/>
    </inputs>
    <outputs>
        <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertions" />
        <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absences" />
        <data format="zip" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" />
    </outputs>
    <tests>
        <test>
            <param name="alignment" value="chr2l_bwa_mem.bam" ftype="bam"/>
            <param name="reference2bit" value="dm6_chr2l.twobit" ftype="twobit"/>

18:e198b686bfe4

<tool id ="run_TEMP" name="TEMP" version="0.2.1">
    <description></description>
    <requirements>
        <!-- The following are classical toolshed packages and should be removed
        once conda is deemed stable-->
        <requirement type="package" version="1.6.922">bioperl</requirement>

        -s $__tool_directory__/scripts
        -r "$te_locations"
        -t "$reference2bit"
        -f "$median_insertsize"
        -c \${GALAXY_SLOTS:-2} &&
        mv alignment.insertion.refined.bp.summary $insertion_summary &&
        mv alignment.absence.refined.bp.summary $absence_summary &&
        tar -czf archive.tar.gz  *insertion* *excision* *absence* && mv archive.tar.gz $archive
    ]]></command>
    <inputs>
        <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
        <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>
        <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/>

        <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum difference between mapping scores"/>
    </inputs>
    <outputs>
        <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertions" />
        <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absences" />
        <data format="tar" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" />
    </outputs>
    <tests>
        <test>
            <param name="alignment" value="chr2l_bwa_mem.bam" ftype="bam"/>
            <param name="reference2bit" value="dm6_chr2l.twobit" ftype="twobit"/>