view macs2_randsample.xml @ 0:fe62ba547975 draft

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<tool id="macs2_randsample" name="MACS2 randsample" version="@VERSION_STRING@.0">
    <description>Randomly sample number or percentage of total reads</description>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <command>
        macs2 randsample
            -t "${ infile }"
            -o "${ outfile }"

        --format '${ infile.extension.upper() }'

        @tag_size@
        #if $method_options.method_options_selector == 'percentage':
            --percentage "${ method_options.percentage }"
        #else:
            --number "${ method_options.number }"
        #end if
    </command>
    <expand macro="stdio" />
    <inputs>
        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
        <expand macro="tag_size" />

        <conditional name="method_options">
            <param name="method_options_selector" type="select" label="Select action to be performed">
                <option value="percentage" selected="true">Percentage</option>
                <option value="number">Number</option>
            </param>
            <when value="percentage">
                    <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" />
            </when>
            <when value="number">
                    <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <!-- No test, due to the randomness -->
    </tests>
    <help>
**What it does**

randsample tool from macs2

@citation@
  </help>
  <expand macro="citations" />
</tool>