view tools/findPeaks.xml @ 58:d602d8b1dc4f

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<tool id="homer_findPeaks" name="find Peaks" version="0.1.2">
    <description></description>
    <requirements>
        <requirement type="package" version="35x1">blat</requirement>
        <requirement type="package" version="2.8.2">weblogo</requirement>
        <requirement type="package" version="9.07">ghostscript</requirement>
    </requirements>
    <!--<version_command></version_command>-->
    <command>
        export PATH=\$PATH:$database.fields.path;

        findPeaks $affected_tag_dir.extra_files_path -o $outputPeakFile

        #if $control_tag_dir:
            -i $control_tag_dir.extra_files_path
        #end if

        #if $logfile_output:
            2> $out_logfile
        #else:
            2>&#38;1
        #end if

    </command>
    <inputs>
        <expand macro="input_choose_homer_version" />
        <param name="affected_tag_dir" format="homer_tagdir" type="data" label="tag directory" help="Must be made with the tool makeTagDirectory" />
        <param name="control_tag_dir" type="data" format="homer_tagdir" optional="True" label="Control tag directory" help="Must be made with makeTagDirectory" />
        <param name="logfile_output" type="boolean" truevalue="" falsevalue="" label="Output HOMER logfile" help=""/>
    </inputs>
    <outputs>
        <data format="txt" name="outputPeakFile" label="${tool.name} on #echo os.path.splitext(str($affected_tag_dir.name))[0]#.txt" />
    </outputs>
    <tests>
        <test>
        </test>
    </tests>

    <help>

  .. class:: infomark

  **Homer findPeaks**

Requires tag directories (see makeTagDirectory)

    </help>
</tool>