comparison deepTools_macros.xml @ 37:7d1521817494 draft

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

36:1de3ede909ef

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">3.0.2</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.0.2">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="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"

                 of the data. Non-covered regions may represent, for
                 example, repetitive regions that should be ignored.
                 (default: False)" />
    </xml>

    <xml name="input_save_matrix_values">
        <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
    </xml>

    <xml name="input_graphic_output_settings">

        <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" />

37:7d1521817494

<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"

                 of the data. Non-covered regions may represent, for
                 example, repetitive regions that should be ignored.
                 (default: False)" />
    </xml>

    <xml name="exactScaling">
        <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
            label="Compute an exact scaling factor"
            help="Compute an exact scaling factor rather than one based on
                  sampled reads. This is only useful in cases where you are
                  filtering some alignments out AND this are both rare and
                  tend to clump together in the genome. In such cases the
                  region-based sampling employed by deepTools would produce
                  inaccurate scaling factors. Note that this option results
                  in the process taking significantly more time to complete." />
    </xml>

    <xml name="input_save_matrix_values">
        <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
    </xml>

    <xml name="input_graphic_output_settings">

        <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" />