comparison macs2_randsample.xml @ 5:beb902da6e5f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b

4:56e104999978

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <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>
    <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>

5:beb902da6e5f

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
        <![CDATA[
        macs2 randsample
            -t '${ infile }'
            -o '${ outfile }'
            --seed '${ seed }'

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

            @tag_size@

        #if $method_options.method_options_selector == 'percentage':
            --percentage '${ method_options.percentage }'
        #else:
            --number '${ method_options.number }'
        #end if
        ]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
        <expand macro="tag_size" />
        <conditional name="method_options">
            <param name="method_options_selector" type="select" label="Select action to be performed">
                <option value="percentage" selected="true">Percentage</option>
                <option value="number">Number</option>
            </param>
            <when value="percentage">
                    <param name="percentage" type="float" value="80.0" label="Percentage of tags you want to keep" help="Percentage of tags you want to keep. Input 80.0 for 80%.(--percentage)"/>
            </when>
            <when value="number">
                    <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" />
            </when>
        </conditional>
        <param name="seed" type="integer" value="1" label="Random seed number" min="0" help="Set the random seed while down sampling data. Must be a positive integer in order to be effective. (--seed)"/>
    </inputs>
    <outputs>
        <data name="outfile" format="bed" label="${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" file="bdgrandsample_output.bed"/>
        </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>