annotate macs2_bdgdiff.xml @ 17:424aefbd7777 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e90e79e18362561d0060d2c162f1938feebdbc29

<tool id="macs2_bdgdiff" name="MACS2 bdgdiff" version="@VERSION_STRING@.1" profile="17.09">
    <description>Differential peak detection based on paired four bedgraph files</description>
    <macros>
        <import>macs2_macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="4.1.3">gawk</requirement>
    </expand>
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command><![CDATA[
        @home_dir@
        macs2 bdgdiff
            --t1 '${ t1 }'
            --t2 '${ t2 }'
            --c1 '${ c1 }'
            --c2 '${ c2 }'
            --cutoff '${ cutoff }'
            --min-len '${ minlen }'
            --depth1 '${ depth.depth1 }'
            --depth2 '${ depth.depth2 }'
            --max-gap '${ maxgap }'
            -o c1.bed c2.bed both.bed &&

            awk '!/^track name/' "c1.bed" > '${ output_cond1 }' &&
            awk '!/^track name/' "c2.bed" > '${ output_cond2 }' &&
            awk '!/^track name/' "both.bed" > '${ output_both }'
    ]]></command>
    <inputs>
        <param name="t1" type="data" format="bedgraph" label="BedGraph for Treatment experiment 1" />
        <param name="t2" type="data" format="bedgraph" label="BedGraph for Treatment experiment 2" />

        <param name="c1" type="data" format="bedgraph" label="BedGraph for Control experiment 1" />
        <param name="c2" type="data" format="bedgraph" label="Bedgraph for Control experiment 2" />

        <param name="cutoff" type="float" label="Cutoff of log10 likelihood ratio cutoff" value="1.0" help="Default=1.0 correspoinding to likelihood ratio of 1,000 (--cutoff)"/>
        <param name="minlen" type="integer" label="Minimum length of differential region" value="200" help=" Try bigger value to remove small regions. Default=200 (--min-len)"/>

        <section name="depth" title="Sequencing depth" expanded="True" help="Sequencing depths will be used to calculate scaling factor for each sample, to down-scale larger sample to the level of smaller one. For example, while comparing condition 1 (10 Million reads) and condition 2 (20 million reads), use --depth1 10 --depth2 20, then pileup value in bedGraph for condition 2 will be divided by 2.">
            <param name="depth1" type="integer" value="1" label="Sequence depth of condition 1 in million reads" help="Default=1 (--depth1)" />
            <param name="depth2" type="integer" value="1" label="Sequence depth of condition 2 in million reads" help="Default=1 (--depth2)" />
        </section>
        <param name="maxgap" type="integer" value="100" label="Maximum gap to merge nearby differential regions" help="Consider a wider gap for broad marks. Maximum gap should be smaller than minimum length. Default=100 (--max-gap)." />


    </inputs>
    <outputs>
        <data name="output_cond1" format="bed" label="${tool.name} on ${on_string} (Condition 1)"/>
        <data name="output_cond2" format="bed" label="${tool.name} on ${on_string} (Condition 2)"/>
        <data name="output_both"  format="bed" label="${tool.name} on ${on_string} (Common)"/>
    </outputs>
    <tests>
        <test>
            <param name="t1" value="bdgdiff_t1.bdg" ftype="bedgraph"/>
            <param name="t2" value="bdgdiff_t2.bdg" ftype="bedgraph"/>
            <param name="c1" value="bdgdiff_c1.bdg" ftype="bedgraph"/>
            <param name="c2" value="bdgdiff_c2.bdg" ftype="bedgraph"/>
            <param name="cutoff" value="1.0"/>
            <param name="minlen" value="200"/>
            <param name="depth1" value="10"/>
            <param name="depth2" value="1"/>
            <param name="maxgap" value="100"/>
            <output name="output_cond1" ftype="bed" value="bdgdiff_output_c1.bed"/>
            <output name="output_cond2">
                <assert_contents>
                    <has_text text="c2.bed1" />
                </assert_contents>
            </output>
            <output name="output_both" ftype="bed" value="bdgdiff_output_both.bed"/>
        </test>
    </tests>
    <help>
    <![CDATA[
**What it does**

This is **bdgdiff** utility from the MACS2_ Package. It performs differential peak detection based on paired four bedgraph files.

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

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