comparison findPeaks.xml @ 12:4356089c8e7f draft

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12:4356089c8e7f

<tool id="homer_findPeaks" name="homer_findPeaks" version="0.1.2">
    <requirements>
        <requirement type="package" version="4.1">homer</requirement>
    </requirements>
    <description>Homer's peakcaller. Requires tag directories (see makeTagDirectory)</description>
    <!--<version_command></version_command>-->
    <command>
        findPeaks $tagDir.extra_files_path $options -o $outputPeakFile

    #if $control_tagDir:
        -i $control_tagDir.extra_files_path
    #end if

        2&gt; $out_log || echo "Error running findPeaks." >&amp;2
    </command>
    <inputs>
        <param format="homerTagDirectory" name="tagDir" type="data" label="tag directory" help="Must be made with homer_makeTagDirectory" />
        <param format="homerTagDirectory" name="control_tagDir" type="data" optional="True" label="Control tag directory" help="Must be made with homer_makeTagDirectory" />
        <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options">
          <sanitizer>
            <valid initial="string.printable">
             <remove value="&apos;"/>
             <remove value="/"/>
            </valid>
            <mapping initial="none">
              <add source="&apos;" target="__sq__"/>
            </mapping>
          </sanitizer>
        </param>
    </inputs>
    <outputs>
        <!--<data format="html" name="html_outfile" label="index" />-->
        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
        <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.txt" />
        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($tagDir.name))[0]#.log" />
    </outputs>
    <tests>
        <test>
            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
        </test>
    </tests>

    <help>

  .. class:: infomark

  **Homer findPeaks**

  For more options, look under: "Command line options for findPeaks"

  http://biowhat.ucsd.edu/homer/ngs/peaks.html

  TIP: use homer_bed2pos and homer_pos2bed to convert between the homer peak positions and the BED format.

    </help>
</tool>