comparison deepTools_macros.xml @ 18:396dfbc32304 draft

planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 72ae8f62333aa38d1c63034ddb37184a0f72c64e-dirty

17:f2f1ca0f032f

<macros>

    <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
    <token name="@WRAPPER_VERSION@">3.0.0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="3.0.0">deeptools</requirement>
            <requirement type="package" version="1.7">samtools</requirement>
        </requirements>
        <expand macro="stdio" />
        <version_command>@BINARY@ --version</version_command>
    </xml>

            #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" &&
                #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

18:396dfbc32304

<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>

            #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