view bed2pos.xml @ 28:f0b5827b6051 draft default tip

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<tool id="homer_bed2pos" name="homer_bed2pos" version="1.0.0">
    <requirements>
        <requirement type="package" version="4.1">homer</requirement>
    </requirements>
    <description></description>
    <!--<version_command></version_command>-->
    <command>
        bed2pos.pl $input_bed 1&gt; $out_pos
        2&gt; $out_log || echo "Error running bed2pos." >&amp;2
    </command>
    <inputs>
        <param format="tabular,bed" name="input_bed" type="data" label="BED file" />
    </inputs>
    <outputs>
        <!--<data format="html" name="html_outfile" label="index" />-->
        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
        <data format="tabular" name="out_pos" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#" />
        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.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

        Converts: BED -(to)-> homer peak positions

        **Homer bed2pos.pl**

        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
    </help>
</tool>