comparison cuffquant_wrapper.xml @ 3:6dc45faebc1d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5

2:b2ee2bef1926

<tool id="cuffquant" name="Cuffquant" version="@VERSION@.0">
    <!-- Wrapper supports Cuffdiff versions 2.2.1 -->
    <description>Precompute gene expression levels</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <version_command>cuffquant 2>&amp;1 | head -n 1</version_command>
    <command>
        cuffquant
            --no-update-check
            --num-threads=\${GALAXY_SLOTS:-4}
            ## Set advanced SE data parameters?
            #if $additional.sAdditional == "Yes":

            #end if
            ## Inputs.
            '$gtf_input'
            #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] )
            '$samplestring'
    </command>
    <inputs>
        <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts"
            help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/>

        <repeat name="samples" title="Replicate" min="1">

3:6dc45faebc1d

<tool id="cuffquant" name="Cuffquant" version="@VERSION@.1">
    <!-- Wrapper supports Cuffdiff versions 2.2.1 -->
    <description>Precompute gene expression levels</description>
    <macros>
      <import>cuff_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <version_command>cuffquant 2>&amp;1 | head -n 1</version_command>
    <command detect_errors="aggressive"><![CDATA[
        cuffquant
            --no-update-check
            --num-threads=\${GALAXY_SLOTS:-4}
            ## Set advanced SE data parameters?
            #if $additional.sAdditional == "Yes":

            #end if
            ## Inputs.
            '$gtf_input'
            #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] )
            '$samplestring'
    ]]></command>
    <inputs>
        <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts"
            help="A transcript annotation (GFF3 or GTF) file produced by cufflinks, cuffcompare, or other source."/>

        <repeat name="samples" title="Replicate" min="1">