annotate sum_fastqc.xml @ 8:5a9a44e23dad draft

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<tool id="sum_fastqc" name="sum_fastqc" version="0.21">
    <description>summarizes raw FASTQC output</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[

      #if $jobtype.select == "single"
        #set inname = $jobtype.file
        #set infile = $jobtype.file
        perl $__tool_directory__/sum_fastqc.pl "$inname" $qset.qscore $infile > sum_fastqc.tab
      #else if $jobtype.select == "col"
        #set inname = $jobtype.coll.name
        #set infile = $jobtype.coll.forward
        #set infile2 = $jobtype.coll.reverse
        perl $__tool_directory__/sum_fastqc.pl "$inname" $qset.qscore $infile $infile2 > sum_fastqc.tab;
      #end if

    ]]></command>
    <inputs>
      <conditional name="jobtype">
        <param name="select" type="select" label="Select Input">
          <option value="single">Raw FASTQC output File</option>
          <option value="col">Pair of raw FASTQC Files</option>
        </param>
        <when value="single">
          <param name="file" type="data" format="txt" label="Raw FASTQC" />
        </when>
        <when value="col">
          <param name="coll" label="Raw FASTQC pair" type="data_collection" format="txt" collection_type="paired" />
        </when>
      </conditional>
      <conditional name="qset">
        <param name="selectq" type="select" label="Single or multiple Q scores">
          <option value="single">Single Q score</option>
          <option value="mul">Multiple Q scores</option>
        </param>
        <when value="single">
          <param name="qscore" type="integer" label="Q score threshold (i.e. reads >= Q score)" value="30">
            <validator type="in_range" message="Must be integer(0,40)." min="0" max="40"/>
          </param>
        </when>
        <when value="mul">
          <param name="qscore" type="text" label="Comma delimited Q score list (e.g. 25,30,35)" value="30"/>
        </when>
      </conditional>
    </inputs>
    <outputs>
      <data format="tabular" name="FASTQC Summary" label="${tool.name} on ${on_string}: Contigs" from_work_dir="*.tab"/>
    </outputs>

    <help><![CDATA[

    ]]></help>
     <citations>
    </citations>
</tool>