annotate pos2bed.xml @ 2:7268cbc535e5 draft

findpeaks and maketagdirectory

<tool id="homer_pos2bed" name="homer_pos2bed" version="0.0.2">
    <requirements>
        <requirement type="package">homer</requirement>
    </requirements>
    <description></description>
    <!--<version_command></version_command>-->
    <command>
        pos2bed.pl $input_peak 1&gt; $out_bed
        2&gt; $out_log || echo "Error running pos2bed." >&amp;2
    </command>
    <inputs>
        <param format="tabular" name="input_peak" type="data" label="Homer peak positions" />
    </inputs>
    <outputs>
        <!--<data format="html" name="html_outfile" label="index" />-->
        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
        <data format="bed" name="out_bed" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.bed" />
        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_peak.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 pos2bed.pl**
        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
    </help>
</tool>