comparison deepTools_macros.xml @ 17:f024daeffbed draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit b1f975422b307927bbbe245d57609e9464d5d5c8-dirty

16:77e1664d66cd

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.5.7</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.5.7">deeptools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </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 are included. The default behavior is to ignore such regions." />
    </xml>

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

    </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 to 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="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="0"
            label="Minimum mapping quality"
            help= "If set, only reads with a mapping quality score higher than this value are considered."/>
    </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 may result in fewer considered regions." />
    </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, so this is only needed for single-end data."/>
    </xml>

    <xml name="scaleFactor">
        <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
            help="The computed scaling factor will be multiplied by this (default 1)." />

        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <when value="No">
            <param argument="--bamfiles" type="data" format="bam" min="@MIN@"
                label="Bam file" multiple="true"
                help=""/>
        </when>
        <when value="Yes">
            <repeat name="multibam_repeats" min="@MIN@" title="BAM Files">
                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
            </repeat>
        </when>
        </conditional>
    </xml>

    <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
        <conditional name="multibigwig_conditional">
        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples 
is vital to you, select Yes below.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <when value="No">
            <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
                label="@LABEL@"
                help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
        </when>
        <when value="Yes">
            <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
                <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
            </repeat>
        </when>
        </conditional>
    </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[

        #import re
        #if $multibam_conditional.orderMatters == "No":
            #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
                ln -s "${bamfile}" "./${counter}.bam" &&
                ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
                #silent $files.append('%s.bam' % $counter)
                #silent $labels.append("'%s'" % identifier)
            #end for
        #else:
            #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
                ln -s "${f.bamfiles}" "./${counter}.bam" &&
                ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
                #silent $files.append('%s.bam' % $counter)
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #end if
]]>
    </token>

        #import re
        #if $multibigwig_conditional.orderMatters == "No":
            #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
                ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
                #silent $files.append('%s_%s.bw' % ($identifier, $counter))
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #else:
            #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
                ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
                #silent $files.append('%s_%s.bw' % ($identifier, $counter))
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #end if
]]>
    </token>

            #end for
            #if $blfiles != ["'None'"]:
                --blackListFileName #echo ' '.join($blfiles)#
            #end if
        #end if
]]> 
    </token>

    <xml name="multiple_bed">
        <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
            label="Regions in BED/GTF format"

        #end for
        #if len($files) > 0:
            --BED #echo ' '.join($files)#
            --regionLabels #echo ' '.join($labels)#
        #end if
]]> 
    </token>

    <xml name="reference_genome_source">
        <conditional name="source">
            <param name="ref_source" type="select" label="Reference genome">

    <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="skipNAs">
        <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"

            </param>
            <when value="no" />
            <when value="yes">
                <yield />
                <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_dpi">
        <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"

        <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">

        </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://matplotlib.org/examples/color/colormaps_reference.html"
               multiple="true">
            <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>

17:f024daeffbed

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">3.0.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.0.0">deeptools</requirement>
            <requirement type="package" version="1.7">samtools</requirement>
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </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/CRAM files are included. The default behavior is to ignore such regions." />
    </xml>

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

    </xml>

    <xml name="extendReads">
        <conditional name="doExtendCustom">
            <param name="doExtend" type="select" label="Extend reads to the given average fragment size."
                help="If selected : Single-end reads and singletons are extended to match the given length and Paired-end reads are extended to match the fragment size.
                     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 to 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="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">maintain the same ordering as the input files</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="0"
            label="Minimum mapping quality"
            help= "If set, only reads with a mapping quality score at least this high are considered."/>
    </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/CRAM files given are ignored. This may result in fewer considered regions." />
    </xml>

    <xml name="fragmentLength">
        <param argument="--fragmentLength" type="integer" min="1" optional="true"
            label="Fragment length used for the sequencing"
            help ="If paired-end reads are used, the fragment length is computed from the BAM/CRAM file, so this is only needed for single-end data."/>
    </xml>

    <xml name="scaleFactor">
        <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
            help="The computed scaling factor will be multiplied by this (default 1)." />

        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <when value="No">
            <param argument="--bamfiles" type="data" format="bam,cram" min="@MIN@"
                label="BAM/CRAM file" multiple="true"
                help=""/>
        </when>
        <when value="Yes">
            <repeat name="multibam_repeats" min="@MIN@" title="BAM/CRAM Files">
                <param argument="--bamfiles" type="data" format="bam,cram" label="BAM/CRAM file" help="" />
            </repeat>
        </when>
        </conditional>
    </xml>

    <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
        <conditional name="multibigwig_conditional">
        <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
is vital to you, select Yes below.">
            <option value="No" selected="true">No</option>
            <option value="Yes">Yes</option>
        </param>
        <when value="No">
            <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
                label="@LABEL@"
                help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
        </when>
        <when value="Yes">
            <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
                <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM/CRAM file using the bamCoverage tool."/>
            </repeat>
        </when>
        </conditional>
    </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>

    <xml name="labelRotation">
        <param argument="--labelRotation" type="integer" value="0"
            label="Rotation of the X-axis labels (in degrees)"
            help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." />
    </xml>


    <token name="@multiple_input_bams@">
<![CDATA[

        #import re
        #if $multibam_conditional.orderMatters == "No":
            #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
                ln -s "${bamfile}" "./${counter}.bam" &&
                #if $bamfile.ext == 'bam':
                    ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
                #else:
                    ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
                #end if
                #silent $files.append("'%s.bam'" % $counter)
                #silent $labels.append("'%s'" % identifier)
            #end for
        #else:
            #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
                ln -s "${f.bamfiles}" "./${counter}.bam" &&
                ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
                #if $f.bamfiles.ext == 'bam':
                    ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
                #else:
                    ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
                #end if
                #silent $files.append("'%s.bam'" % $counter)
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #end if
]]>
    </token>

        #import re
        #if $multibigwig_conditional.orderMatters == "No":
            #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
                ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
                #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #else:
            #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
                ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
                #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
                #silent $labels.append("'%s'" % $identifier)
            #end for
        #end if
]]>
    </token>

            #end for
            #if $blfiles != ["'None'"]:
                --blackListFileName #echo ' '.join($blfiles)#
            #end if
        #end if
]]>
    </token>

    <xml name="multiple_bed">
        <param argument="--BED" type="data" format="bed,gtf" min="1" multiple="true"
            label="Regions in BED/GTF format"

        #end for
        #if len($files) > 0:
            --BED #echo ' '.join($files)#
            --regionLabels #echo ' '.join($labels)#
        #end if
]]>
    </token>

    <xml name="reference_genome_source">
        <conditional name="source">
            <param name="ref_source" type="select" label="Reference genome">

    <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.
                    We provide a table of useful sizes here: http://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html">
                <option value="93260000">ce10 (93260000)</option>
                <option value="130428560">dm3 (130428560)</option>
                <option value="125464728">dm6 (125464728)</option>
                <option value="2685511504" selected="true">hg19/GRCh37 (2685511504)</option>
                <option value="2701495761">GRCh38/hg38 (2701495761)</option>
                <option value="2304947926">GRCm37/mm9 (2304947926)</option>
                <option value="2308125349">GRCm38/mm10 (2308125349)</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: 130428560, hg19: 2685511504, mm9: 2304947926"/>
            </when>
            <when value="93260000" />
            <when value="130428560" />
            <when value="125464728" />
            <when value="2685511504" />
            <when value="2701495761" />
            <when value="2304947926" />
            <when value="2308125349" />
        </conditional>
    </xml>

    <xml name="skipNAs">
        <param argument="--skipNAs" type="boolean" truevalue="--skipNAs" falsevalue="" checked="False"

            </param>
            <when value="no" />
            <when value="yes">
                <yield />
                <param name="saveSortedRegions" type="boolean"
                       argument="--outFileSortedRegions"
                       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" help="Note that the plotly output can be very large and not all options are supported.">
            <option value="png" selected="true">png</option>
            <option value="pdf">pdf</option>
            <option value="svg">svg</option>
            <option value="eps">eps</option>
            <option value="plotly">plotly</option>
        </param>
    </xml>

    <xml name="output_dpi">
        <param argument="--dpi" name="dpi" type="integer" value="200" size="3" optional="True"

        <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" />
            </change_format>
        </data>
    </xml>

    <xml name="output_save_matrix_values">

        </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://matplotlib.org/examples/color/colormaps_reference.html">
            <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>