comparison deepTools_macros.xml @ 2:000ef7d1b4ea draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289

1:0240a81c3ae6

<macros>

    <xml name="advancedOpt_scaffold">
        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>

                    <add value="|"/>
                    <add value=":"/>
                 </valid>
            </sanitizer>
        </param>
    </xml>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.4.2</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="package" version="2.4.2">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 bases)"

    </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" />

            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="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)"/>

    <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 "${f.bamfiles}" "./${counter}.bam" &&
                ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
                #silent $files.append('%s.bam' % $counter)
                #silent $labels.append("'%s'" % ($f.bamfiles.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 "${f.bigwigfiles}" "${counter}.bw" &&
                #silent $files.append('%s.bw' % $counter)
                #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name))
            #end for
        #end if
]]>
    </token>

2:000ef7d1b4ea

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">2.5.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2.7.10">python</requirement>
            <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
            <yield />
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

    <xml name="advancedOpt_scaffold">
        <conditional name="advancedOpt">
            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                <option value="no" selected="true">no</option>

                    <add value="|"/>
                    <add value=":"/>
                 </valid>
            </sanitizer>
        </param>
    </xml>

    <xml name="smoothLength">
        <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
            label="Smooth values using the following length (in bases)"

    </xml>

    <xml name="fragLength">
        <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
            label="Minimum fragment length for inclusion."
            help="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="A value of 0 (the default) is equivalent to no maximum." />
    </xml>

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

            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)." />
    </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)"/>

    <token name="@multiple_input_bams@">
<![CDATA[
        #set files=[]
        #set labels=[]
        #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>

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