Mercurial > repos > bgruening > deeptools_bam_coverage

comparison deepTools_macros.xml @ 14:6a676cb3fa8e draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit b5fc4073c884a2d6a4092ea85150db1971010f28
author bgruening
date Sun, 14 May 2017 18:19:48 -0400
parents 22bfbb186bf1
children 5d11599b8a7d
comparison
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13:c192acaeef84 14:6a676cb3fa8e
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@">2.5.0</token> 4 <token name="@WRAPPER_VERSION@">2.5.1.0</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="2.7.10">python</requirement>
8 <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement> 7 <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
9 <yield /> 8 <yield />
10 </requirements> 9 </requirements>
11 <expand macro="stdio" /> 10 <expand macro="stdio" />
12 <version_command>@BINARY@ --version</version_command> 11 <version_command>@BINARY@ --version</version_command>
21 <when value="no" /> 20 <when value="no" />
22 <when value="yes"> 21 <when value="yes">
23 <yield/> 22 <yield/>
24 </when> 23 </when>
25 </conditional> 24 </conditional>
25 </xml>
26
27 <token name="@PLOTWIDTHHEIGHT@">
28 --plotWidth '$advancedOpt.plotWidth'
29 --plotHeight '$advancedOpt.plotHeight'
30 </token>
31
32 <xml name="plotWidthHeight" tokens="PLOTWIDTH,PLOTHEIGHT">
33 <param argument="--plotHeight" type="float" value="@PLOTHEIGHT@" min="1.0"
34 label="Plot height"
35 help="Height in cm. The default for the plot height is @PLOTHEIGHT@ centimeters. The minimum value is 1 cm." />
36
37 <param argument="--plotWidth" type="float" value="@PLOTWIDTH@" min="1.0"
38 label="Plot width"
39 help="Width in cm. The default value is @PLOTWIDTH@ centimeters. The minimum value is 1 cm." />
26 </xml> 40 </xml>
27 41
28 <token name="@ADVANCED_OPTS_READ_PROCESSING@"> 42 <token name="@ADVANCED_OPTS_READ_PROCESSING@">
29 #if $advancedOpt.doExtendCustom.doExtend == 'custom': 43 #if $advancedOpt.doExtendCustom.doExtend == 'custom':
30 --extendReads $advancedOpt.doExtendCustom.extendReadsValue 44 --extendReads $advancedOpt.doExtendCustom.extendReadsValue
367 <citation type="doi">10.1093/nar/gkw257</citation> 381 <citation type="doi">10.1093/nar/gkw257</citation>
368 <yield /> 382 <yield />
369 </citations> 383 </citations>
370 </xml> 384 </xml>
371 385
372 <xml name="multiple_input_bams"> 386 <xml name="multiple_input_bams" tokens="MIN">
373 <conditional name="multibam_conditional"> 387 <conditional name="multibam_conditional">
374 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below."> 388 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples is vital to you, select Yes below.">
375 <option value="No" selected="true">No</option> 389 <option value="No" selected="true">No</option>
376 <option value="Yes">Yes</option> 390 <option value="Yes">Yes</option>
377 </param> 391 </param>
378 <when value="No"> 392 <when value="No">
379 <param argument="--bamfiles" type="data" format="bam" min="1" 393 <param argument="--bamfiles" type="data" format="bam" min="@MIN@"
380 label="Bam file" multiple="true" 394 label="Bam file" multiple="true"
381 help=""/> 395 help=""/>
382 </when> 396 </when>
383 <when value="Yes"> 397 <when value="Yes">
384 <repeat name="multibam_repeats" min="1" title="BAM Files"> 398 <repeat name="multibam_repeats" min="@MIN@" title="BAM Files">
385 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" /> 399 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
386 </repeat> 400 </repeat>
387 </when> 401 </when>
388 </conditional> 402 </conditional>
389 </xml> 403 </xml>
390 404
391 <xml name="multiple_input_bams_min2"> 405 <xml name="multiple_input_bigwigs" tokens="MIN,LABEL,TITLE">
392 <conditional name="multibam_conditional">
393 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
394 is vital to you, select Yes below.">
395 <option value="No" selected="true">No</option>
396 <option value="Yes">Yes</option>
397 </param>
398 <when value="No">
399 <param argument="--bamfiles" type="data" format="bam" min="2"
400 label="Bam file" multiple="true"
401 help=""/>
402 </when>
403 <when value="Yes">
404 <repeat name="multibam_repeats" min="2" title="BAM Files">
405 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
406 </repeat>
407 </when>
408 </conditional>
409 </xml>
410
411 <xml name="multiple_input_bigwigs">
412 <conditional name="multibigwig_conditional"> 406 <conditional name="multibigwig_conditional">
413 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples 407 <param name="orderMatters" type="select" label="Sample order matters" help="By default, the order of samples given to the program is dependent on their order in your history. If the order of the samples
414 is vital to you, select Yes below."> 408 is vital to you, select Yes below.">
415 <option value="No" selected="true">No</option> 409 <option value="No" selected="true">No</option>
416 <option value="Yes">Yes</option> 410 <option value="Yes">Yes</option>
417 </param> 411 </param>
418 <when value="No"> 412 <when value="No">
419 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" 413 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="@MIN@"
420 label="Bigwig file" 414 label="@LABEL@"
421 help="A Bigwig file."/> 415 help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
422 </when> 416 </when>
423 <when value="Yes"> 417 <when value="Yes">
424 <repeat name="multibigwig_repeats" min="2" title="BigWig files"> 418 <repeat name="multibigwig_repeats" min="@MIN@" title="@TITLE@">
425 <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/> 419 <param argument="--bigwigfiles" type="data" format="bigwig" label="@LABEL@" help="You can generate a bigWig file from a BAM file using the bamCoverage tool."/>
426 </repeat> 420 </repeat>
427 </when> 421 </when>
428 </conditional> 422 </conditional>
429 </xml> 423 </xml>
430 424
465 #set files=[] 459 #set files=[]
466 #set labels=[] 460 #set labels=[]
467 #import re 461 #import re
468 #if $multibigwig_conditional.orderMatters == "No": 462 #if $multibigwig_conditional.orderMatters == "No":
469 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): 463 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
470 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier)) 464 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
471 ln -s "${bigwig}" "${counter}.bw" && 465 ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
472 #silent $files.append('%s.bw' % $counter) 466 #silent $files.append('%s_%s.bw' % ($identifier, $counter))
473 #silent $labels.append("'%s'" % $identifier) 467 #silent $labels.append("'%s'" % $identifier)
474 #end for 468 #end for
475 #else: 469 #else:
476 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): 470 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
477 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) 471 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
478 ln -s "${f.bigwigfiles}" "${counter}.bw" && 472 ln -f -s "${f.bigwigfiles}" "${identifier}_${counter}.bw" &&
479 #silent $files.append('%s.bw' % $counter) 473 #silent $files.append('%s_%s.bw' % ($identifier, $counter))
480 #silent $labels.append("'%s'" % $identifier) 474 #silent $labels.append("'%s'" % $identifier)
481 #end for 475 #end for
482 #end if 476 #end if
483 ]]> 477 ]]>
484 </token> 478 </token>