comparison deepTools_macros.xml @ 11:3909b643c81c draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a

10:848ce8f81e6e

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">3.1.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.1.0">deeptools</requirement>
            <requirement type="package" version="1.7">samtools</requirement>
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </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" />
        <param argument="--exonID" optional="True" value="exon" type="text"
            label="exon 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 exons. CDS would be another common value for this. Default: exon" />
        <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"

        <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
            label="Image dpi" help=""/>
    </xml>

    <xml name="output_image_file_format">
        <data format="png" name="outFileName" label="${tool.name} image">
            <change_format>
                <when input="output.outFileFormat" value="pdf" format="pdf" />
                <when input="output.outFileFormat" value="svg" format="svg" />
                <when input="output.outFileFormat" value="eps" format="eps" />
                <when input="output.outFileFormat" value="plotly" format="html" />
            </change_format>
        </data>
    </xml>

    <xml name="output_image_file_format_not_nested">
        <data format="png" name="outFileName" label="${tool.name} image">
            <change_format>
                <when input="outFileFormat" value="pdf" format="pdf" />
                <when input="outFileFormat" value="svg" format="svg" />
                <when input="outFileFormat" value="eps" format="eps" />
                <when input="outFileFormat" value="plotly" format="html" />

11:3909b643c81c

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">3.1.2.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.1.2">deeptools</requirement>
            <requirement type="package" version="1.7">samtools</requirement>
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </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="transcript 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" />
        <param argument="--exonID" optional="True" value="exon" type="text"
            label="exon 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 exons. CDS would be another common value for this. Default: exon" />
        <param argument="--transcript_id_designator" optional="True" value="transcript_id" type="text"

        <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"
            label="Image dpi" help=""/>
    </xml>

    <xml name="output_image_file_format">
        <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
            <change_format>
                <when input="output.outFileFormat" value="pdf" format="pdf" />
                <when input="output.outFileFormat" value="svg" format="svg" />
                <when input="output.outFileFormat" value="eps" format="eps" />
                <when input="output.outFileFormat" value="plotly" format="html" />
            </change_format>
        </data>
    </xml>

    <xml name="output_image_file_format_not_nested">
        <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
            <change_format>
                <when input="outFileFormat" value="pdf" format="pdf" />
                <when input="outFileFormat" value="svg" format="svg" />
                <when input="outFileFormat" value="eps" format="eps" />
                <when input="outFileFormat" value="plotly" format="html" />