Mercurial > repos > bgruening > deeptools_bam_coverage

comparison deepTools_macros.xml @ 19:3033c3fba046 draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
author bgruening
date Thu, 05 Apr 2018 10:58:15 -0400
parents 609399927ca5
children 827fe3df85c3
comparison
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18:609399927ca5 19:3033c3fba046
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@">3.0.1</token> 4 <token name="@WRAPPER_VERSION@">3.0.2</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.0.1">deeptools</requirement> 7 <requirement type="package" version="3.0.2">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>
116 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;."> 116 help="This is useful when testing parameters to reduce the time required. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;.">
117 <sanitizer> 117 <sanitizer>
118 <valid initial="string.letters,string.digits"> 118 <valid initial="string.letters,string.digits">
119 <add value="|"/> 119 <add value="|"/>
120 <add value=":"/> 120 <add value=":"/>
121 <add value="."/>
121 </valid> 122 </valid>
122 </sanitizer> 123 </sanitizer>
123 </param> 124 </param>
124 </xml> 125 </xml>
125 126
441 #set labels=[] 442 #set labels=[]
442 #import re 443 #import re
443 #if $multibam_conditional.orderMatters == "No": 444 #if $multibam_conditional.orderMatters == "No":
444 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): 445 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
445 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier)) 446 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
446 ln -s "${bamfile}" "./${counter}.bam" && 447 ln -s '${bamfile}' './${counter}.bam' &&
447 #if $bamfile.ext == 'bam': 448 #if $bamfile.ext == 'bam':
448 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && 449 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
449 #else: 450 #else:
450 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && 451 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
451 #end if 452 #end if
453 #silent $labels.append("'%s'" % identifier) 454 #silent $labels.append("'%s'" % identifier)
454 #end for 455 #end for
455 #else: 456 #else:
456 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): 457 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
457 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) 458 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
458 ln -s "${f.bamfiles}" "./${counter}.bam" && 459 ln -s '${f.bamfiles}' './${counter}.bam' &&
459 #if $f.bamfiles.ext == 'bam': 460 #if $f.bamfiles.ext == 'bam':
460 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' && 461 ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' &&
461 #else: 462 #else:
462 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' && 463 ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' &&
463 #end if 464 #end if
474 #set labels=[] 475 #set labels=[]
475 #import re 476 #import re
476 #if $multibigwig_conditional.orderMatters == "No": 477 #if $multibigwig_conditional.orderMatters == "No":
477 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): 478 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
478 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) 479 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
479 ln -f -s "${bigwig}" "${identifier}_${counter}.bw" && 480 ln -f -s '${bigwig}' '${identifier}_${counter}.bw' &&
480 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) 481 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
481 #silent $labels.append("'%s'" % $identifier) 482 #silent $labels.append("'%s'" % $identifier)
482 #end for 483 #end for
483 #else: 484 #else:
484 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): 485 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
485 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) 486 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
486 ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" && 487 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
487 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) 488 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
488 #silent $labels.append("'%s'" % $identifier) 489 #silent $labels.append("'%s'" % $identifier)
489 #end for 490 #end for
490 #end if 491 #end if
491 ]]> 492 ]]>
554 555
555 <token name="@reference_genome_source@"> 556 <token name="@reference_genome_source@">
556 #if $source.ref_source=="history": 557 #if $source.ref_source=="history":
557 --genome $source.input1 558 --genome $source.input1
558 #else: 559 #else:
559 --genome "$source.input1_2bit.fields.path" 560 --genome '$source.input1_2bit.fields.path'
560 #end if 561 #end if
561 </token> 562 </token>
562 563
563 <xml name="effectiveGenomeSize"> 564 <xml name="effectiveGenomeSize">
564 <conditional name="effectiveGenomeSize"> 565 <conditional name="effectiveGenomeSize">