comparison deepTools_macros.xml @ 26:ac3e9fc67755 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca

25:43e379eea838

            </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>

    <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">

                #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>

                #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>

26:ac3e9fc67755

            </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="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">

                #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>

                #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>