comparison deepTools_macros.xml @ 3:be8d749ea54b draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit a92b8557d0985038d24daaab2996fbf8e4cd323f

2:fee7b464d8e9

            </when>
        </conditional>
    </xml>

    <token name="@ADVANCED_OPTS_READ_PROCESSING@">
        --extendReads $advancedOpt.extendReads
        $advancedOpt.ignoreDuplicates
        $advancedOpt.centerReads
        #if $advancedOpt.minMappingQuality:
            --minMappingQuality '$advancedOpt.minMappingQuality'
        #end if

        <expand macro="plotTitle" />
        <expand macro="plotNumbers" />
    </xml>

    <token name="@HEATMAP_OPTIONS@">
        #if $zMin:
            --zMin $zMin
        #end if
        #if $zMax:
            --zMax $zMax
        #end if
        --colorMap '$colorMap'
        $plotNumbers
        --plotTitle $plotTitle
    </token>


    <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>

    <xml name="zMin_zMax">
        <param argument="--zMin" type="integer" value="" optional="true" label="Minimum value for the heatmap intensities"
            help="If not specified the value is set automatically."/>
        <param argument="--zMax" type="integer" value="" optional="true" label="Maximum value for the heatmap intensities"
            help="If not specified the value is set automatically."/>
    </xml>

    <xml name="region_limit_operation">
        <param argument="--region" type="text" value=""

            label="Plot the correlation value"
            help="If set, then the correlation number is plotted on top of the heatmap."/>
    </xml>

    <xml name="extendReads">
        <param argument="--extendReads" type="integer" value="" optional="True"
            label="Extend reads to the given average fragment size"
            help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
                    By default *each* read mate is extended.
                    This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
                    Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value.
                    Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not
                    recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data."/>
    </xml>

    <xml name="corMethod">
        <param argument="--corMethod" type="select" label="Correlation method">
            <option value="spearman" selected="True">Spearman</option>

            <yield />
        </citations>
    </xml>

    <xml name="multiple_input_bams">
        <param argument="--bamfiles" type="data" format="bam"
            label="Bam file" multiple="true"
            help="The BAM file must be sorted."/>
    </xml>

    <xml name="multiple_input_bigwigs">
        <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True"
            label="Bigwig file"
            help="The Bigwig file must be sorted."/>
    </xml>

    <xml name="plotTitle">

            <when value="121400000" />
            <when value="93260000" />
        </conditional>
    </xml>

    <xml name="image_file_format">
        <param argument="--outFileFormat" type="select" label="Image file format">
            <option value="png" selected="true">png</option>
            <option value="pdf">pdf</option>
            <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

                <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
            </when>
        </conditional>
    </xml>

    <xml name="input_image_file_format">
        <param name="outFileFormat" type="select" label="Image file format">
            <option value="png" selected="true">png</option>
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
            <option value="eps">eps</option>
            <option value="emf">emf</option>
        </param>
    </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="emf" format="emf" />
            </change_format>
        </data>
    </xml>

    <xml name="output_save_matrix_values">

3:be8d749ea54b

            </when>
        </conditional>
    </xml>

    <token name="@ADVANCED_OPTS_READ_PROCESSING@">
        #if $advancedOpt.doExtendCustom.doExtend == 'custom':
            --extendReads $advancedOpt.doExtendCustom.extendReadsValue
        #else if $advancedOpt.doExtendCustom.doExtend == 'yes':
            --extendReads
        #end if
        $advancedOpt.ignoreDuplicates
        $advancedOpt.centerReads
        #if $advancedOpt.minMappingQuality:
            --minMappingQuality '$advancedOpt.minMappingQuality'
        #end if

        <expand macro="plotTitle" />
        <expand macro="plotNumbers" />
    </xml>

    <token name="@HEATMAP_OPTIONS@">
        #if $plotting_type.zMin:
            --zMin $plotting_type.zMin
        #end if
        #if $plotting_type.zMax:
            --zMax $plotting_type.zMax
        #end if
        --colorMap '$plotting_type.colorMap'
        $plotting_type.plotNumbers
        --plotTitle '$plotting_type.plotTitle'
    </token>


    <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>

    <xml name="zMin_zMax">
        <param argument="--zMin" type="float" value="" optional="true" label="Minimum value for the heatmap intensities"
            help="If not specified the value is set automatically."/>
        <param argument="--zMax" type="float" value="" optional="true" label="Maximum value for the heatmap intensities"
            help="If not specified the value is set automatically."/>
    </xml>

    <xml name="region_limit_operation">
        <param argument="--region" type="text" value=""

            label="Plot the correlation value"
            help="If set, then the correlation number is plotted on top of the heatmap."/>
    </xml>

    <xml name="extendReads">
        <conditional name="doExtendCustom">
            <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
                help="(1) Single-end reads and singletons are extended to match this length. (2) Paired-end reads are extended to match the fragment size, regardless of what is set here.
                        By default *each* read mate is extended.
                        This can be modified using the SAM flags (see --samFlagInclude and --samFlagExclude options) to keep only the first or the second mate.
                        Unmated reads, mate reads that map on different chromosomes or too far apart are extended to the given value.
                        Reads are only extended if --extendReads is set to a value greater than the read length. *NOTE*: For spliced-read data, this option is not
                        recommended as it will extend reads over skipped regions, e.g. introns in RNA-seq data.">
                <option value="no" selected="True">No extension. The default value and most typically appropriate.</option>
                <option value="yes">Paired-end extension. Suitable only for paired-end datasets.</option>
                <option value="custom">A custom length, which will be applied to ALL reads.</option>
            </param>
            <when value="no" />
            <when value="yes" />
            <when value="custom">
                <param name="extendReadsValue" type="integer" value="300" min="1"
                    label="Extend reads to the given average fragment size"
                    help="Extend all reads to this length" />
            </when>
        </conditional>
    </xml>

    <xml name="corMethod">
        <param argument="--corMethod" type="select" label="Correlation method">
            <option value="spearman" selected="True">Spearman</option>

            <yield />
        </citations>
    </xml>

    <xml name="multiple_input_bams">
        <param argument="--bamfiles" type="data" format="bam" min="2"
            label="Bam file" multiple="true"
            help="The BAM file must be sorted."/>
    </xml>

    <xml name="multiple_input_bigwigs">
        <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
            label="Bigwig file"
            help="The Bigwig file must be sorted."/>
    </xml>

    <xml name="plotTitle">

            <when value="121400000" />
            <when value="93260000" />
        </conditional>
    </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

                <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
            </when>
        </conditional>
    </xml>


    <xml name="input_image_file_format">
        <param argument="--outFileFormat" type="select" label="Image file format">
            <option value="png" selected="true">png</option>
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
            <option value="eps">eps</option>
        </param>
    </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" />
            </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" />
            </change_format>
        </data>
    </xml>

    <xml name="output_save_matrix_values">