comparison macs2_macros.xml @ 18:640d3af5d833 draft

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

17:424aefbd7777

<macros>
    <token name="@VERSION_STRING@">2.1.1.20160309</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION_STRING@">macs2</requirement>
            <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">

            <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 (--mfold)" >
            <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>

        #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="integer" label="Tag size" value="" optional="true"
               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=" You can set this parameter as the medium fragment size expected from sonication or size selection. (--bw)" />
    </xml>

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

18:640d3af5d833

<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">

            <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>

        #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 }'