annotate macs2_predictd.xml @ 18:640d3af5d833 draft

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

<tool id="macs2_predictd" name="MACS2 predictd" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
    <description>Predict 'd' or fragment size from alignment results</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 predictd

        -i ${ ' '.join(["'%s'" % $x for $x in $infiles ]) }
        @tag_size@
        @effective_genome_size@
        --bw '${ band_width }'
        @mfold_command@
        --d-min $d_min
        @buffer_size@

        ## remove the timepoint and strip the output
        2>&1 | awk -F: '{print $4}' | awk '{$1=$1}1'

        > '${ outfile }'

        &&

        Rscript predictd
    ]]></command>
    <inputs>
        <param name="infiles" type="data" format="bam,bed" multiple="True"
               label="ChIP-seq alignment file"
               help="If multiple files are given, then they will all be read and combined. Note that pair-end data is not supposed to work with this command. (-i)" />
        <expand macro="conditional_effective_genome_size" />
        <expand macro="tag_size" />
        <expand macro="band_width" />
        <expand macro="mfold_options" />
        <expand macro="fragment_size"/>
        <expand macro="buffer_size"/>
    </inputs>

    <outputs>
        <data name="outfile" format="txt" label="${tool.name} on ${on_string} - d value" />
        <data name="outfile_image" from_work_dir="predictd_model.pdf" format="pdf" label="${tool.name} on ${on_string} - X-correlation image" />
    </outputs>
    <tests>
        <test>
            <param name="infiles" value="Control_200K.bed,ChIP_200K.bed" ftype="bed" />
            <param name="effective_genome_size_options_selector" value="user_defined" />
            <param name="gsize" value="3300000000" />
            <param name="tsize" value=""/>
            <param name="band_width" value="300"/>
            <param name="lower" value="5"/>
            <param name="upper" value="50"/>
            <assert_command>
                <has_text text="--buffer-size"/>
                <has_text text="--d-min"/>
            </assert_command>
            <output name="outfile">
                <assert_contents>
                    <has_line line="# predicted fragment length is 284 bps" />
                </assert_contents>
            </output>
            <output name="outfile_image" file="predictd_on_ChIP_200K_and_Control_200K.pdf" compare="sim_size" ftype="pdf"/>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

This is **predictd** utility from the MACS2_ Package. It predicts the *d* value or fragment size from alignment results.

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

@citation@
]]>

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