annotate macs2_macros.xml @ 0:fe62ba547975 draft

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<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.1.0">macs2</requirement>
            <requirement type="package" version="1.7.1">numpy</requirement>
            <requirement type="package" version="0.12.0">scipy</requirement>
            <yield />
        </requirements>
    </xml>

    <token name="@VERSION_STRING@">2.1.0.20140616</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 NNNN 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.
                    See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes. (--gsize)">
                <option value="2451960000">Human (2,451,960,000)</option>
                <option value="2150570000">Mouse (2,150,570,000)</option>
                <option value="121400000">Fly (121,400,000)</option>
                <option value="93260000">Worm (93,260,000)</option>
                <option value="user_defined">User defined</option>
            </param>
            <when value="user_defined">
                <param name="gsize" type="integer" size="12" 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>

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

    <xml name="tag_size">
        <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will override the auto detected tag size. Per default that option is deactivated: -1.0 (--tsize)" />
    </xml>
    <xml name="band_width">
        <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
            help="This value is only used while building the shifting model. (--bw)" />
    </xml>

    <token name="@tag_size@">
        #if $tsize == -1.0:
            --tsize "${ 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@">
------

**Citation**

For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

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>
        </citations>
    </xml>
</macros>