comparison deepTools_macros.xml @ 10:2a56d1eb6c46 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09

9:4efe24a9739e

            </sanitizer>
        </param>
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.3.6</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="package" version="2.3.6">deepTools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

            <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">

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

    <xml name="multiple_input_bams">
        <param argument="--bamfiles" type="data" format="bam" min="1"
            label="Bam file" multiple="true"
            help=""/>
    </xml>

    <xml name="multiple_input_bams_min2">
        <param argument="--bamfiles" type="data" format="bam" min="2"
            label="Bam file" multiple="true"
            help=""/>
    </xml>

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

    <xml name="plotTitle">
        <param argument="--plotTitle" type="text" value="" size="30" optional="True"
            label="Title of the plot"

    <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="blacklist">
        <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"

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            </sanitizer>
        </param>
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.4.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="package" version="2.4.1">deeptools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

            <option value="sum">sum</option>
            <option value="region_length">region length</option>
        </param>
    </xml>

    <xml name="sortRegionsComputeMatrix">
        <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="keep" selected="true">maintain the same ordering as the input files</option>
            <option value="descend">descending order</option>
            <option value="ascend">ascending order</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">descending order</option>
            <option value="ascend">ascending order</option>
        </param>
    </xml>

    <xml name="minMappingQuality">

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

    <xml name="multiple_input_bams">
        <conditional name="multibam_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="--bamfiles" type="data" format="bam" min="1"
                label="Bam file" multiple="true"
                help=""/>
        </when>
        <when value="Yes">
            <repeat name="multibam_repeats" min="1" title="BAM Files">
                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
            </repeat>
        </when>
        </conditional>
    </xml>

    <xml name="multiple_input_bams_min2">
        <conditional name="multibam_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="--bamfiles" type="data" format="bam" min="2"
                label="Bam file" multiple="true"
                help=""/>
        </when>
        <when value="Yes">
            <repeat name="multibam_repeats" min="2" title="BAM Files">
                <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
            </repeat>
        </when>
        </conditional>
    </xml>

    <xml name="multiple_input_bigwigs">
        <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="2"
                label="Bigwig file"
                help="A Bigwig file."/>
        </when>
        <when value="Yes">
            <repeat name="multibigwig_repeats" min="2" title="BigWig files">
                <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
            </repeat>
        </when>
        </conditional>
    </xml>

    <xml name="plotTitle">
        <param argument="--plotTitle" type="text" value="" size="30" optional="True"
            label="Title of the plot"

    <token name="@multiple_input_bams@">
<![CDATA[
        #set files=[]
        #set labels=[]
        #if $multibam_conditional.orderMatters == "No":
            #for $counter, $bamfile in enumerate($multibam_conditional.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
        #else:
            #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
                ln -s "${f.bamfile}" "./${counter}.bam" &&
                ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
                #silent $files.append('%s.bam' % $counter)
                #silent $labels.append("'%s'" % ($f.bamfile.display_name))
            #end for
        #end if
]]>
    </token>

    <token name="@multiple_input_bigwigs@">
<![CDATA[
        #set files=[]
        #set labels=[]
        #if $multibigwig_conditional.orderMatters == "No":
            #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
                ln -s "${bigwig}" "${counter}.bw" &&
                #silent $files.append('%s.bw' % $counter)
                #silent $labels.append("'%s'" % ($bigwig.display_name))
            #end for
        #else:
            #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
                ln -s "${f.bigwig}" "${counter}.bw" &&
                #silent $files.append('%s.bw' % $counter)
                #silent $labels.append("'%s'" % ($f.bigwig.display_name))
            #end for
        #end if
]]>
    </token>

    <xml name="blacklist">
        <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"