view makeTagDirectory.xml @ 10:7efeace8bd32 draft

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<tool id="homer_makeTagDirectory" name="homer_makeTagDirectory" version="1.0.1">
    <requirements>
        <requirement type="package" >homer</requirement>
    </requirements>
    <description>Simple wrapper for makeTagDirectory. Used by findPeaks</description>
    <!--<version_command></version_command>-->
    <command interpreter="python">makeTagDirectory.py ${tagDir.files_path} 
        #for $alignF in $alignmentFiles
          $alignF.file -f $alignF.file.ext
        #end for
          -o $tagDir
        2&gt; $out_log || echo "Error running homer_makeTagDirectory." >&amp;2

    </command>
    <inputs>
        <param name="title" label="Name for the output tag directory" type="text" default="Homer TagDirectory" />
        <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>
        <repeat name="alignmentFiles" title="Alignment Files">
          <param name="file" label="Add file" type="data" format="sam,bed" />
        </repeat>
    </inputs>
    <outputs>
        <!--<data format="homerTagDirectory" name="tagDir" label="${title} tag directory" />-->
        <data format="html" name="tagDir" label="${title} tag directory" />
        <data format="txt" name="out_log" label="${title}.log" />
        <!--<data format="html" name="html_outfile" label="index" />-->
        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
    </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 makeTagDirectory**

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

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


    </help>
</tool>