view annotatePeaks.xml @ 0:2103c773690f draft

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<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.2">
    <requirements>
        <requirement type="package">homer</requirement>
    </requirements>
    <description></description>
    <!--<version_command></version_command>-->
    <command>
        annotatePeaks.pl $input_bed $genome_selector 1&gt; $out_annotated
        2&gt; $out_log || echo "Error running annotatePeaks." >&amp;2
    </command>
    <inputs>
        <param format="tabular,bed" name="input_bed" type="data" label="Homer peak positions or BED format" />
        <param name="genome_selector" type="select" label="Genome version">
            <option value="hg19" selected="true">hg19</option>
        </param>
    </inputs>
    <outputs>
        <!--<data format="html" name="html_outfile" label="index" />-->
        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
        <data format="csv" name="out_annotated" label="${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
        http://biowhat.ucsd.edu/homer/ngs/annotation.html


    </help>
</tool>