Mercurial > repos > bgruening > deeptools_plot_pca
comparison deepTools_macros.xml @ 18:396dfbc32304 draft
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 72ae8f62333aa38d1c63034ddb37184a0f72c64e-dirty
author | bgruening |
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date | Fri, 02 Mar 2018 15:56:38 -0500 |
parents | f2f1ca0f032f |
children | d9376d223fad |
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17:f2f1ca0f032f | 18:396dfbc32304 |
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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 |