comparison deepTools_macros.xml @ 8:dc8d6e07d829 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 2c5f94de9ddf6798e49b7e9c340c841ca2bfbcfe

7:b4886e1369c4

            --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" />

            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="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="Region of the genome to limit the operation to"
            help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
            <sanitizer>
                <valid initial="string.letters,string.digits">
                    <add value="|"/>
                 </valid>
            </sanitizer>
        </param>
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.2.3</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="binary">@BINARY@</requirement>
            <requirement type="package" version="2.2.3">deepTools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

        <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."/>

            <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 with a mapping quality score higher than this value are considered."/>
    </xml>

    <xml name="skipZeros">

            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="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" />

                <option value="yes">yes</option>
            </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>

            <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>

            </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://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>

8:dc8d6e07d829

            --samFlagInclude $advancedOpt.samFlagInclude
        #end if
        #if $advancedOpt.samFlagExclude:
            --samFlagExclude $advancedOpt.samFlagExclude
        #end if
        #if $advancedOpt.minFragmentLength:
            --minFragmentLength $advancedOpt.minFragmentLength
        #end if
        #if $advancedOpt.maxFragmentLength:
            --maxFragmentLength $advancedOpt.maxFragmentLength
        #end if
    </token>

    <token name="@ADVANCED_OPTS_GTF@">
        $advancedOpt.metagene
        #if $advancedOpt.transcriptID:
            --transcriptID $advancedOpt.transcriptID
        #end if
        #if $advancedOpt.exonID:
            --exonID $advancedOpt.exonID
        #end if
        #if $advancedOpt.transcript_id_designator:
            --transcript_id_designator $advancedOpt.transcript_id_designator
        #end if
    </token>

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

            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."/>
        <param argument="--zMax" type="text" 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 time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
            <sanitizer>
                <valid initial="string.letters,string.digits">
                    <add value="|"/>
                    <add value=":"/>
                 </valid>
            </sanitizer>
        </param>
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.3.5</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="package" version="2.3.5">deepTools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

        <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="fragLength">
        <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
            label="Minimum fragment length for inclusion."
            help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
        <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
            label="Maximum fragment length for inclusion."
            help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." />
    </xml>

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

    <xml name="gtf_options">
        <param argument="--metagene" type="boolean" truevalue="--boolean" 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"
            label="transcriptID key designator"
            help="Each region has an ID (e.g., ACTB) assigned to it, which for BED files is either column 4 (if it exists)
                  or the interval bounds. For GTF files this is instead stored in the last column as a key:value pair (e.g.,
                  as 'transcript_id ACTB', for a key of transcript_id and a value of ACTB). In some cases it can be
                  convenient to use a different identifier. To do so, set this to the desired key. Default: transcript_id" />
    </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."/>

            <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">

            ln -s "${bigwig}" "${counter}.bw" &&
            #silent $files.append('%s.bw' % $counter)
            #silent $labels.append("'%s'" % ($bigwig.display_name))
        #end for
]]>
    </token>

    <xml name="blacklist">
        <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"
            label="Blacklisted regions in BED/GTF format"
            help="One or more files containing regions to exclude from the analysis" />
    </xml>

    <token name="@blacklist@">
<![CDATA[
        #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None':
            #set blfiles=[]
            #for $f in $advancedOpt.blackListFileName:
                #silent $blfiles.append("'%s'" % $f)
            #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"
            help="One or more files containing regions to include in the analysis" />
    </xml>

    <token name="@multiple_bed@">
<![CDATA[
        #set files=[]
        #set labels=[]
        #for $f in $BED:
            #silent $files.append("'%s'" % $f)
            #silent $labels.append("'%s'" % $f.display_name)
        #end for
        #if len($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">

                <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" />

                <option value="yes">yes</option>
            </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>

            <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"
            label="Image dpi" help=""/>
    </xml>

    <xml name="output_image_file_format">
        <data format="png" name="outFileName" label="${tool.name} image">
            <change_format>

            </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://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>