view macs2_randsample.xml @ 18:640d3af5d833 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"

<tool id="macs2_randsample" name="MACS2 randsample" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>Randomly sample number or percentage of total reads</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @home_dir@
        macs2 randsample
            -i '${ infile }'
            -o '${ outfile }'
            --seed '${ seed }'

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

            @tag_size@

        #if $method_options.method_options_selector == 'percentage':
            --percentage '${ method_options.percentage }'
        #else:
            --number '${ method_options.number }'
        #end if
        ]]></command>
    <inputs>
        <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" />
        <expand macro="tag_size" />
        <conditional name="method_options">
            <param name="method_options_selector" type="select" label="Select action to be performed">
                <option value="percentage" selected="true">Percentage</option>
                <option value="number">Number</option>
            </param>
            <when value="percentage">
                    <param name="percentage" type="float" value="80.0" label="Percentage of tags you want to keep" help="Percentage of tags you want to keep. Input 80.0 for 80%.(--percentage)"/>
            </when>
            <when value="number">
                    <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" />
            </when>
        </conditional>
        <param name="seed" type="integer" value="1" label="Random seed number" min="0" help="Set the random seed while down sampling data. Must be a positive integer in order to be effective. (--seed)"/>
    </inputs>
    <outputs>
        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="infile" value="ChIP_200K.bed" ftype="bed" />
            <param name="method_options_selector" value="percentage" />
            <param name="percentage" value="80.0" />
            <param name="seed" value="1" />
            <output name="outfile">
                <assert_contents>
                    <has_text text="27179762" />
                    <has_text text="4441986" />
                    <has_size value="4787911" delta="500"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
        <![CDATA[
**What it does**

This is **randsample** utility from the MACS2_ Package. It randomly samples reads by number or percentage from an input file.

.. _MACS2: https://github.com/taoliu/MACS

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