view deepTools_macros.xml @ 0:3b40996fc4f1 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit e1fd513c18e0d5b53071d99f539ac3509ced01aa-dirty

<macros>

    <xml name="advancedOpt_scaffold">
        <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">
                <yield/>
            </when>
        </conditional>
    </xml>

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

    <xml name="heatmap_options">
        <expand macro="zMin_zMax" />
        <expand macro="colorMap" />
        <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
    </token>

        <expand macro="plotTitle" />
        <expand macro="plotNumbers" />
        <conditional name="output">
            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <expand macro="input_image_file_format"/>
                <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>

    <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="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 &quot;chr10&quot; or &quot;chr10:456700:891000&quot;." />
    </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>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

    <xml name="smoothLength">
        <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
            label="Smooth values using the following length (in bp)"
            help ="The smooth length defines a window, larger than the bin size, to average the number of reads. For example, if the bin size is set to 20 bp and the smooth length is set to 60 bp, then, for each bin size the average of it and its left and right neighbors is considered. Any value smaller than the bin size will be ignored and no smoothing will be applied."/>
    </xml>


    <xml name="kmeans_clustering">
        <conditional name="used_multiple_regions">
            <param name="used_multiple_regions_options" type="select" 
                label="Did you compute the matrix with more than one groups of regions?"
                help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
                <option value="yes">Yes, I used multiple groups of regions</option>
                <option value="no">No, I used only one group</option>
            </param>
            <when value="no">
                <conditional name="clustering">
                    <param name="clustering_options" type="select" label="Clustering algorithm">
                        <option value="none">No clustering</option>
                        <option value="kmeans">Kmeans clustering</option>
                    </param>
                    <when value="kmeans">
                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" 
                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
                    </when>
                    <when value="none" />
                </conditional>
            </when>
            <when value="yes" />
        </conditional>
    </xml>

    <token name="@KMEANS_CLUSTERING@">
        #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no':
            #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans':
                #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0:
                    --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans
                #end if
            #end if
        #end if
    </token>

    <xml name="samFlags">
        <param argument="--samFlagInclude" type="integer" optional="True" value=""
            label="Include reads based on the SAM flag"
            help= "For example, to get only reads that are the first mate use a flag of 64. This is useful to count properly paired reads only once, otherwise the second mate will be also considered for the coverage."/>
        <param argument="--samFlagExclude" type="integer" optional="True" value=""
            label="Exclude reads based on the SAM flag"
            help= "For example, to get only reads that map to the forward strand, use --samFlagExclude 16, where 16 is the SAM flag for reads that map to the reverse strand."/>
    </xml>

    <xml name="read_processing_options">
        <expand macro="extendReads" />
        <expand macro="ignoreDuplicates" />
        <expand macro="centerReads" />
        <expand macro="minMappingQuality" />
        <expand macro="samFlags" />
    </xml>

    <xml name="plotNumbers">
        <param argument="--plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue=""
            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>
            <option value="pearson">Pearson</option>
        </param>
    </xml>

    <xml name="distanceBetweenBins">
        <param argument="--distanceBetweenBins" type="integer" value="0" min="0"
            label="Distance between bins"
            help="By default, bamCorrelate considers consecutive bins of
                the specified 'Bin size'. However, to reduce the
                computation time, a larger distance between bins can
                by given. Larger distances result in less bins being
                considered."/>
    </xml>

    <xml name="centerReads">
        <param argument="--centerReads" type="boolean" truevalue="--centerReads" falsevalue=""
            label="Center regions with respect to the fragment length"
            help="For paired-end data, the read is centered at the fragment length defined by the two ends of the fragment. For single-end data, the given fragment length is used. This option is useful to get a sharper signal around enriched regions. "/>
    </xml>

    <xml name="ignoreDuplicates">
        <param argument="--ignoreDuplicates" type="boolean" truevalue="--ignoreDuplicates" falsevalue=""
            label="Ignore duplicates"
            help="If set, reads that have the same orientation and start position will be considered only once. If reads are paired, the mate position also has to coincide to ignore a read." />
    </xml>

    <xml name="sortUsing">
        <param argument="--sortUsing" type="select" label="Method used for sorting"
            help="For each row the method is computed.">
            <option value="mean" selected="true">mean</option>
            <option value="median">median</option>
            <option value="min">min</option>
            <option value="max">max</option>
            <option value="sum">sum</option>
            <option value="region_length">region length</option>
        </param>
    </xml>

    <xml name="sortRegions">
        <param argument="--sortRegions" type="select" label="Sort regions"
            help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
            <option value="no">no ordering</option>
            <option value="descend" selected="true">descending order</option>
            <option value="ascend">ascending order</option>
        </param>
    </xml>

    <xml name="minMappingQuality">
        <param argument="--minMappingQuality" type="integer" optional="true" value="1" min="1"
            label="Minimum mapping quality"
            help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
    </xml>

    <xml name="skipZeros">
        <param argument="--skipZeros" type="boolean" truevalue="--skipZeros" falsevalue=""
            label ="Skip zeros"
            help ="If set, then zero counts that happen for *all* BAM files given are ignored. This might have the effect that fewer regions are considered than indicated in the option where the number of samples is defined." />
    </xml>

    <xml name="fragmentLength">
        <param argument="--fragmentLength" type="integer" value="300" min="1"
            label="Fragment length used for the sequencing"
            help ="If paired-end reads are used, the fragment length is computed from the BAM file."/>
    </xml>

    <xml name="scaleFactor">
        <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
            help="When used in combination with --normalizeTo1x or
                --normalizeUsingRPKM, the computed scaling factor will
                be multiplied by the given scale factor." />
    </xml>

    <xml name="scaleFactors">
        <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
        <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
            <exit_code range=":-1" />
            <regex match="Error:" />
            <regex match="Exception:" />
            <regex match="EXception:" />
            <regex match="Traceback" />
        </stdio>
    </xml>

    <xml name="pseudocount">
        <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
    </xml>

    <token name="@REFERENCES@">

.. class:: infomark

For more information on the tools, please visit our `help site`_.

If you would like to give us feedback or you run into any trouble, please send an email to [e-mail]

This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_.

.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/
.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de
.. _help site: https://github.com/fidelram/deepTools/wiki/

    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1093/nar/gku365</citation>
            <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">
        <param argument="--plotTitle" type="text" value="" size="30" optional="True"
            label="Title of the plot"
            help="Title of the plot, to be printed on top of the generated image." />
    </xml>

    <token name="@multiple_input_bams@">
<![CDATA[
        #set files=[]
        #set labels=[]
        #for $counter, $bamfile in enumerate($bamfiles):
            ln -s "${bamfile}" "./${counter}.bam" &&
            ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
            #silent $files.append('%s.bam' % $counter)
            #silent $labels.append('%s' % ($bamfile.display_name))
        #end for
]]>
    </token>

    <token name="@multiple_input_bigwigs@">
<![CDATA[
        #set files=[]
        #set labels=[]
        #for $counter, $bigwig in enumerate($bigwigfiles):
            ln -s "${bigwig}" "${counter}.bw" &&
            #silent $files.append('%s.bw' % $counter)
            #silent $labels.append('%s' % ($bigwig.display_name))
        #end for
]]>
    </token>

    <xml name="reference_genome_source">
        <conditional name="source">
            <param name="ref_source" type="select" label="Reference genome">
                <option value="cached">locally cached</option>
                <option value="history">in your history</option>
            </param>
            <when value="cached">
                <param name="input1_2bit" type="select" label="Using reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
                    <options from_data_table="lastz_seqs">
                        <filter type="sort_by" column="1" />
                        <validator type="no_options" message="No indexes are available." />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
            </when>
        </conditional>
    </xml>

    <token name="@reference_genome_source@">
    #if $source.ref_source=="history":
        --genome $source.input1
    #else:
        --genome "${source.input1_2bit.fields.path}"
    #end if
    </token>

    <xml name="effectiveGenomeSize">
        <conditional name="effectiveGenomeSize">
            <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
                help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. 
                    Also, if repetitive regions were not included in the mapping of reads, the effective genome size needs to be adjusted accordingly. 
                    See Table 2 of http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0030377 or http://www.nature.com/nbt/journal/v27/n1/fig_tab/nbt.1518_T1.html for several effective genome sizes.">
                <option value="93260000">ce10 (93260000)</option>
                <option value="121400000">dm3 (121400000)</option>
                <option value="2451960000" selected="true">hg19 (2451960000)</option>
                <option value="2150570000">mm9 (2150570000)</option>
                <option value="specific">user specified</option>
            </param>
            <when value="specific">
                <param argument="--effectiveGenomeSize" type="integer" value="" label="Effective genome size" help="e.g. ce10: 93260000, dm3: 121400000, hg19: 2451960000, mm9: 2150570000"/>
            </when>
            <when value="2150570000" />
            <when value="2451960000" />
            <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="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>

    <xml name="input_graphic_output_settings">
        <conditional name="output" >
            <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="no" />
            <when value="yes">
                <yield />
                <param name="saveData" type="boolean" label="Save the data underlying the average profile"/>
                <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">
        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveMatrix'] is True
            ))
            </filter>
        </data>
    </xml>

    <xml name="output_graphic_outputs">
        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveData'] is True
            ))
            </filter>
        </data>
        <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
            <filter>
            ((
                output['showOutputSettings'] == 'yes' and 
                output['saveSortedRegions'] is True
            ))
            </filter>
        </data>
    </xml>

    <xml name="colorMap">
        <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
            <option value="RdYlBu" selected="true">RdYlBu</option>
            <option value="Accent">Accent</option>
            <option value="Spectral">Spectral</option>
            <option value="Set1">Set1</option>
            <option value="Set2">Set2</option>
            <option value="Set3">Set3</option>
            <option value="Dark2">Dark2</option>
            <option value="Reds">Reds</option>
            <option value="Oranges">Oranges</option>
            <option value="Greens">Greens</option>
            <option value="Blues">Blues</option>
            <option value="Greys">Greys</option>
            <option value="Purples">Purples</option>
            <option value="Paired">Paired</option>
            <option value="Pastel1">Pastel1</option>
            <option value="Pastel2">Pastel2</option>
            <option value="spring">spring</option>
            <option value="summer">summer</option>
            <option value="autumn">autumn</option>
            <option value="winter">winter</option>
            <option value="hot">hot</option>
            <option value="coolwarm">coolwarm</option>
            <option value="cool">cool</option>
            <option value="seismic">seismic</option>
            <option value="terrain">terrain</option>
            <option value="ocean">ocean</option>
            <option value="rainbow">rainbow</option>
            <option value="bone">bone</option>
            <option value="flag">flag</option>
            <option value="prism">prism</option>
            <option value="cubehelix">cubehelix</option>
            <option value="binary">binary</option>
            <option value="pink">pink</option>
            <option value="gray">gray</option>
            <option value="copper">copper</option>
            <option value="BrBG">BrBG</option>
            <option value="BuGn">BuGn</option>
            <option value="BuPu">BuPu</option>
            <option value="GnBu">GnBu</option>
            <option value="OrRd">OrRd</option>
            <option value="PiYG">PiYG</option>
            <option value="PRGn">PRGn</option>
            <option value="PuOr">PuOr</option>
            <option value="PuRd">PuRd</option>
            <option value="PuBu">PuBu</option>
            <option value="RdBu">RdBu</option>
            <option value="RdGy">RdGy</option>
            <option value="RdPu">RdPu</option>
            <option value="YlGn">YlGn</option>
            <option value="PuBuGn">PuBuGn</option>
            <option value="RdYlGn">RdYlGn</option>
            <option value="YlGnBu">YlGnBu</option>
            <option value="YlOrBr">YlOrBr</option>
            <option value="YlOrRd">YlOrRd</option>
            <option value="gist_gray">gist_gray</option>
            <option value="gist_stern">gist_stern</option>
            <option value="gist_earth">gist_earth</option>
            <option value="gist_yarg">gist_yarg</option>
            <option value="gist_ncar">gist_ncar</option>
            <option value="gist_rainbow">gist_rainbow</option>
            <option value="gist_heat">gist_heat</option>
            <option value="gnuplot">gnuplot</option>
            <option value="gnuplot2">gnuplot2</option>
            <option value="CMRmap">CMRmap</option>
            <option value="bwr">bwr</option>
            <option value="hsv">hsv</option>
            <option value="brg">brg</option>
            <option value="jet">jet</option>
            <option value="afmhot">afmhot</option>
            <option value="Accent_r">Accent reversed</option>
            <option value="Spectral_r">Spectral reversed</option>
            <option value="Set1_r">Set1 reversed</option>
            <option value="Set2_r">Set2 reversed</option>
            <option value="Set3_r">Set3 reversed</option>
            <option value="Dark2_r">Dark2 reversed</option>
            <option value="Reds_r">Reds reversed</option>
            <option value="Oranges_r">Oranges reversed</option>
            <option value="Greens_r">Greens reversed</option>
            <option value="Blues_r">Blues reversed</option>
            <option value="Greys_r">Greys reversed</option>
            <option value="Purples_r">Purples reversed</option>
            <option value="Paired_r">Paired reversed</option>
            <option value="Pastel1_r">Pastel1 reversed</option>
            <option value="Pastel2_r">Pastel2 reversed</option>
            <option value="spring_r">spring reversed</option>
            <option value="summer_r">summer reversed</option>
            <option value="autumn_r">autumn reversed</option>
            <option value="winter_r">winter reversed</option>
            <option value="hot_r">hot reversed</option>
            <option value="coolwarm_r">coolwarm reversed</option>
            <option value="cool_r">cool reversed</option>
            <option value="seismic_r">seismic reversed</option>
            <option value="terrain_r">terrain reversed</option>
            <option value="ocean_r">ocean reversed</option>
            <option value="rainbow_r">rainbow reversed</option>
            <option value="bone_r">bone reversed</option>
            <option value="flag_r">flag reversed</option>
            <option value="prism_r">prism reversed</option>
            <option value="cubehelix_r">cubehelix reversed</option>
            <option value="binary_r">binary reversed</option>
            <option value="pink_r">pink reversed</option>
            <option value="gray_r">gray reversed</option>
            <option value="copper_r">copper reversed</option>
            <option value="BrBG_r">BrBG reversed</option>
            <option value="BuGn_r">BuGn reversed</option>
            <option value="BuPu_r">BuPu reversed</option>
            <option value="GnBu_r">GnBu reversed</option>
            <option value="OrRd_r">OrRd reversed</option>
            <option value="PiYG_r">PiYG reversed</option>
            <option value="PRGn_r">PRGn reversed</option>
            <option value="PuOr_r">PuOr reversed</option>
            <option value="PuRd_r">PuRd reversed</option>
            <option value="PuBu_r">PuBu reversed</option>
            <option value="RdBu_r">RdBu reversed</option>
            <option value="RdGy_r">RdGy reversed</option>
            <option value="RdPu_r">RdPu reversed</option>
            <option value="YlGn_r">YlGn reversed</option>
            <option value="PuBuGn_r">PuBuGn reversed</option>
            <option value="RdYlBu_r">RdYlBu reversed</option>
            <option value="RdYlGn_r">RdYlGn reversed</option>
            <option value="YlGnBu_r">YlGnBu reversed</option>
            <option value="YlOrBr_r">YlOrBr reversed</option>
            <option value="YlOrRd_r">YlOrRd reversed</option>
            <option value="gist_gray_r">gist_gray reversed</option>
            <option value="gist_stern_r">gist_stern reversed</option>
            <option value="gist_earth_r">gist_earth reversed</option>
            <option value="gist_yarg_r">gist_yarg reversed</option>
            <option value="gist_ncar_r">gist_ncar reversed</option>
            <option value="gist_rainbow_r">gist_rainbow reversed</option>
            <option value="gist_heat_r">gist_heat reversed</option>
            <option value="gnuplot_r">gnuplot reversed</option>
            <option value="gnuplot2_r">gnuplot2 reversed</option>
            <option value="CMRmap_r">CMRmap reversed</option>
            <option value="bwr_r">bwr reversed</option>
            <option value="hsv_r">hsv reversed</option>
            <option value="brg_r">brg reversed</option>
            <option value="jet_r">jet reversed</option>
            <option value="afmhot_r">afmhot reversed</option>
        </param>

    </xml>

</macros>