<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.4">
    <requirements>
        <requirement type="package" version="4.1">homer</requirement>
    </requirements>
    <description></description>
    <!--<version_command></version_command>-->
    <command>
        annotatePeaks.pl $input_bed $genome_selector 1&gt; $out_annotated
        2&gt; $out_log || echo "Error running annotatePeaks." >&amp;2
    </command>
    <inputs>
        <param format="tabular,bed" name="input_bed" type="data" label="Homer peaks OR BED format"/>
        <param name="genome_selector" type="select" label="Genome version">
            <option value="hg19" selected="true">hg19</option>
        </param>
        <param type="text" name="options" label="Extra options" value="" help="Go to link below for more options">
          <sanitizer>
            <valid initial="string.printable">
             <remove value="&apos;"/>
             <remove value="/"/>
            </valid>
            <mapping initial="none">
              <add source="&apos;" target="__sq__"/>
            </mapping>
          </sanitizer>
        </param>
    </inputs>
    <outputs>
        <!--<data format="html" name="html_outfile" label="index" />-->
        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
        <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" />
        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.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 annoatePeaks**

        More information on accepted formats and options

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

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

    </help>
</tool>