comparison deepTools_macros.xml @ 19:f011488450e6 draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754

18:2c04ee4b0174

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">3.0.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.0.1">deeptools</requirement>
            <requirement type="package" version="1.7">samtools</requirement>
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

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

        #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" &&
                #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 $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" &&
                #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

        #set labels=[]
        #import re
        #if $multibigwig_conditional.orderMatters == "No":
            #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
                ln -f -s "${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 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">

19:f011488450e6

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">3.0.2</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.0.2">deeptools</requirement>
            <requirement type="package" version="1.7">samtools</requirement>
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

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

        #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' &&
                #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 $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' &&
                #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

        #set labels=[]
        #import re
        #if $multibigwig_conditional.orderMatters == "No":
            #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
                #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
                ln -f -s '${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 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">