annotate macs2_macros.xml @ 18:640d3af5d833 draft

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

<macros>
    <token name="@TOOL_VERSION@">2.2.7.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">macs2</requirement>
            <requirement type="package" version="3.4">r-base</requirement>
            <yield />
        </requirements>
    </xml>
    <xml name="bio_tools">
        <xrefs>
            <xref type="bio.tools">macs</xref>
        </xrefs>
    </xml>
    <token name="@home_dir@"><![CDATA[
        export PYTHON_EGG_CACHE=`pwd` &&
    ]]></token>

    <xml name="conditional_effective_genome_size">
        <conditional name="effective_genome_size_options">
            <param name="effective_genome_size_options_selector" type="select" label="Effective genome size"
                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of Ns that should be discarded.
                Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. Sizes are from the MACS2 website (--gsize)">
                <option value="2700000000">H. sapiens (2.7e9)</option>
                <option value="1870000000">M. musculus (1.87e9)</option>
                <option value="120000000">D. melanogaster (1.2e8)</option>
                <option value="90000000">C. elegans (9e7)</option>
                <option value="user_defined">User defined</option>
            </param>
            <when value="2700000000" />
            <when value="1870000000" />
            <when value="120000000" />
            <when value="90000000" />
            <when value="user_defined">
                <param name="gsize" type="integer" label="Effective genome size" value=""/>
            </when>
        </conditional>
    </xml>

    <xml name="keep_duplicates">
        <conditional name="keep_dup_options">
            <param name="keep_dup_options_selector" type="select" label="How many duplicate tags at the exact same location are allowed?"
                help="The default 'auto' option calculates the maximum tags at the exact same location based on binomial distribution using 1e-5 as pvalue cutoff. The 'all' option keeps every tags. If an integer is given, at most this number of tags will be kept at the same location. The default is to keep one tag at the same location. (--keep-dup 1)">
                <option value="1" selected="true">1</option>
                <option value="all">all</option>
                <option value="auto">auto</option>
                <option value="user">user defined</option>
            </param>
            <when value="user">
                <param name="user_keepdup" type="integer" value="1" label="Keep at most this number of tags at the exact same location"
                    help=""/>
            </when>
            <when value="1" />
            <when value="all" />
            <when value="auto" />
        </conditional>
    </xml>

    <xml name="mfold_options">
        <section name="mfold" title="Mfold settings" expanded="True" 
            help="Select the regions within MFOLD range of highconfidence enrichment ratio against background to build model. Fold-enrichment in regions must be lower than upper limit, and higher than the lower limit. Default is 5 for lower and 50 for upper" >
            <param name="lower" type="integer" value="5" label="Set lower mfold bound" />
            <param name="upper" type="integer" value="50" label="Set upper mfold bound" />
        </section>
    </xml>

    <token name="@mfold_command@">
        --mfold '${mfold.lower}' '${mfold.upper}'
    </token>

    <token name="@effective_genome_size@">
        #if $effective_genome_size_options.effective_genome_size_options_selector == "user_defined":
            --gsize '${ effective_genome_size_options.gsize }'
        #else:
            --gsize '${ effective_genome_size_options.effective_genome_size_options_selector }'
        #end if
    </token>

    <xml name="buffer_size">
            <param argument="--buffer-size" type="integer" min="0" value="100000" label="Buffer size" 
                help="Buffer size for incrementally increasing internal array size to store reads alignment information. In most cases, you don't have to change this parameter.
                    However, if there are large number of chromosomes/contigs/scaffolds in your alignment, it's recommended to specify a smaller buffer size in order to
                    decrease memory usage (but it will take longer time to read alignment files)." />
    </xml>

    <token name="@buffer_size@">
        --buffer-size $buffer_size
    </token>

    <xml name="version_command">
        <version_command>macs2 --version</version_command>
    </xml>

    <xml name="tag_size">
        <param argument="--tsize" type="integer" label="Tag size" value="" optional="true"
               help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 " />
    </xml>
    <xml name="band_width">
        <param name="band_width" type="integer" value="300"
               label="Band width for picking regions to compute fragment size"
               help=" You can set this parameter as the medium fragment size expected from sonication or size selection. (--bw)" />
    </xml>

    <xml name="fragment_size">
        <param argument="--d-min" type="integer" value="20"
            label="Minimum fragment size in basepair"
            help="Any predicted fragment size less than this will be excluded."/>
    </xml>

    <token name="@tag_size@">
        #if $tsize:
            --tsize '${ tsize }'
        #end if
    </token>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>

    <token name="@citation@">
------

Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.

    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/gb-2008-9-9-r137</citation>
            <citation type="doi">10.1038/nprot.2012.101</citation>
        </citations>
    </xml>
</macros>