comparison macs2_macros.xml @ 53:8f6b37d29df5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2

52:6c9ea5f92ddb

            <requirement type="package" version="3.4">r-base</requirement>
            <yield />
        </requirements>
    </xml>

    <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. (--gsize)">
                <option value="2451960000">H. sapiens (2,451,960,000)</option>
                <option value="2150570000">M. musculus (2,150,570,000)</option>
                <option value="121400000">D. melanogaster (121,400,000)</option>
                <option value="93260000">C. elegans (93,260,000)</option>
                <option value="12400000">S. cerevisiae (12,400,000)</option>
                <option value="user_defined">User defined</option>
            </param>
            <when value="2451960000" />
            <when value="2150570000" />
            <when value="121400000" />
            <when value="93260000" />
            <when value="12400000" />
            <when value="user_defined">
                <param name="gsize" type="integer" label="Effective genome size" value=""/>
            </when>
        </conditional>
    </xml>

53:8f6b37d29df5

            <requirement type="package" version="3.4">r-base</requirement>
            <yield />
        </requirements>
    </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>