comparison deepTools_macros.xml @ 16:10ef0a306a46 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4abb1e731efdaa32fadb32c9e23883f7c17fb85c

15:81b1e3e1fc6c

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.5.1.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.5.1">deeptools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

        <expand macro="samFlags" />
        <expand macro="fragLength" />
    </xml>

    <xml name="gtf_options">
        <param argument="--metagene" type="boolean" truevalue="--boolean" falsevalue=""
            label="Use a metagene model"
            help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
        <param argument="--transcriptID" optional="True" value="transcript" type="text"
            label="trascript designator"
            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />

16:10ef0a306a46

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.5.7</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.5.7">deeptools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

        <expand macro="samFlags" />
        <expand macro="fragLength" />
    </xml>

    <xml name="gtf_options">
        <param argument="--metagene" type="boolean" truevalue="--metagene" falsevalue=""
            label="Use a metagene model"
            help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
        <param argument="--transcriptID" optional="True" value="transcript" type="text"
            label="trascript designator"
            help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />