comparison deepTools_macros.xml @ 1:66947f20a9a8 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4fc171a2e9d37ef865695a04ff1b12068d8fe427

0:af2607db5c89

                <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
                <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
            </when>
        </conditional>

<!--
            $mode.advancedOpt.includeZeros


        #if $plotTitle and str($plotTitle).strip() != "":
            - -plotTitle '$plotTitle'
        #end if


-->

    <xml name="bigwigCorrelate_mode_actions">
        <expand macro="region_limit_operation" />

        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <expand macro="includeZeros" />
                <expand macro="zMin_zMax" />
                <expand macro="colorMap" />
                <expand macro="plotTitle" />
                <expand macro="plotNumbers" />
            </when>
        </conditional>
    </xml>

    <xml name="includeZeros">
        <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
            label="Include zeros"
            help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />
    </xml>

            label="Region of the genome to limit the operation to"
            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." />
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">1.5.11</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="binary">@BINARY@</requirement>
            <requirement type="package" version="2.0">deepTools</requirement>

            <option value="svg">svg</option>
            <option value="eps">eps</option>
        </param>
    </xml>

    <xml name="keepNAs">
        <param argument="--keepNAs" type="boolean" truevalue="--keepNAs" falsevalue="" checked="False"
            label="Treat missing data as zero"
            help="If set, missing data (NAs) will be treated as zeros.
                The default is to ignore missing data and not included
                in the output file. Missing data is defined as those
                bins for which no overlapping reads are found." />
    </xml>

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

1:66947f20a9a8

                <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
                <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
            </when>
        </conditional>

    <xml name="includeZeros">
        <param argument="--includeZeros" type="boolean" truevalue="--includeZeros" falsevalue=""
            label="Include zeros"
            help="If set, then regions with zero counts for *all* BAM files given are included. The default behavior is to ignore those cases." />
    </xml>

            label="Region of the genome to limit the operation to"
            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example "chr10" or "chr10:456700:891000"." />
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.0.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="binary">@BINARY@</requirement>
            <requirement type="package" version="2.0">deepTools</requirement>

            <option value="svg">svg</option>
            <option value="eps">eps</option>
        </param>
    </xml>

    <xml name="skipNAs">
        <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"
            label="Ignore missing data?"
            help="This parameter determines if non-covered regions
                 (regions without overlapping reads) in a bam/bigWig file
                 should be skipped. The default is to treat those
                 regions as having a value of zero. The decision to
                 skip non-covered regions depends on the interpretation
                 of the data. Non-covered regions may represent for
                 example repetitive regions that want to be skipped.
                 (default: False)" />
    </xml>

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