Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize

comparison deepTools_macros.xml @ 18:2c04ee4b0174 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 72ae8f62333aa38d1c63034ddb37184a0f72c64e-dirty
author bgruening
date Fri, 02 Mar 2018 15:05:10 -0500
parents 68932756bf49
children f011488450e6
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17:68932756bf49 18:2c04ee4b0174
1 <macros> 1 <macros>
2 2
3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> 3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
4 <token name="@WRAPPER_VERSION@">3.0.0</token> 4 <token name="@WRAPPER_VERSION@">3.0.1</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.0.0">deeptools</requirement> 7 <requirement type="package" version="3.0.1">deeptools</requirement>
8 <requirement type="package" version="1.7">samtools</requirement> 8 <requirement type="package" version="1.7">samtools</requirement>
9 </requirements> 9 </requirements>
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <version_command>@BINARY@ --version</version_command> 11 <version_command>@BINARY@ --version</version_command>
12 </xml> 12 </xml>
454 #end for 454 #end for
455 #else: 455 #else:
456 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): 456 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
457 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) 457 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
458 ln -s "${f.bamfiles}" "./${counter}.bam" && 458 ln -s "${f.bamfiles}" "./${counter}.bam" &&
459 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
460 #if $f.bamfiles.ext == 'bam': 459 #if $f.bamfiles.ext == 'bam':
461 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' && 460 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
462 #else: 461 #else:
463 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' && 462 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
464 #end if 463 #end if