Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize

comparison deepTools_macros.xml @ 11:82c669810520 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca
author bgruening
date Tue, 24 Jan 2017 04:50:24 -0500
parents 2a56d1eb6c46
children 0ed472892e76
comparison
equal deleted inserted replaced
10:2a56d1eb6c46 11:82c669810520
96 </sanitizer> 96 </sanitizer>
97 </param> 97 </param>
98 </xml> 98 </xml>
99 99
100 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token> 100 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
101 <token name="@WRAPPER_VERSION@">2.4.1</token> 101 <token name="@WRAPPER_VERSION@">2.4.2</token>
102 <xml name="requirements"> 102 <xml name="requirements">
103 <requirements> 103 <requirements>
104 <requirement type="package" version="2.7.10">python</requirement> 104 <requirement type="package" version="2.7.10">python</requirement>
105 <requirement type="package" version="2.4.1">deeptools</requirement> 105 <requirement type="package" version="2.4.2">deeptools</requirement>
106 <yield /> 106 <yield />
107 </requirements> 107 </requirements>
108 <expand macro="stdio" /> 108 <expand macro="stdio" />
109 <version_command>@BINARY@ --version</version_command> 109 <version_command>@BINARY@ --version</version_command>
110 </xml> 110 </xml>
297 297
298 <xml name="sortRegions"> 298 <xml name="sortRegions">
299 <param argument="--sortRegions" type="select" label="Sort regions" 299 <param argument="--sortRegions" type="select" label="Sort regions"
300 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region."> 300 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
301 <option value="no">no ordering</option> 301 <option value="no">no ordering</option>
302 <option value="descend">descending order</option> 302 <option value="descend" selected="true">descending order</option>
303 <option value="ascend">ascending order</option> 303 <option value="ascend">ascending order</option>
304 </param> 304 </param>
305 </xml> 305 </xml>
306 306
307 <xml name="minMappingQuality"> 307 <xml name="minMappingQuality">
448 #silent $files.append('%s.bam' % $counter) 448 #silent $files.append('%s.bam' % $counter)
449 #silent $labels.append("'%s'" % ($bamfile.display_name)) 449 #silent $labels.append("'%s'" % ($bamfile.display_name))
450 #end for 450 #end for
451 #else: 451 #else:
452 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): 452 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
453 ln -s "${f.bamfile}" "./${counter}.bam" && 453 ln -s "${f.bamfiles}" "./${counter}.bam" &&
454 ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" && 454 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
455 #silent $files.append('%s.bam' % $counter) 455 #silent $files.append('%s.bam' % $counter)
456 #silent $labels.append("'%s'" % ($f.bamfile.display_name)) 456 #silent $labels.append("'%s'" % ($f.bamfiles.display_name))
457 #end for 457 #end for
458 #end if 458 #end if
459 ]]> 459 ]]>
460 </token> 460 </token>
461 461
469 #silent $files.append('%s.bw' % $counter) 469 #silent $files.append('%s.bw' % $counter)
470 #silent $labels.append("'%s'" % ($bigwig.display_name)) 470 #silent $labels.append("'%s'" % ($bigwig.display_name))
471 #end for 471 #end for
472 #else: 472 #else:
473 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): 473 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
474 ln -s "${f.bigwig}" "${counter}.bw" && 474 ln -s "${f.bigwigfiles}" "${counter}.bw" &&
475 #silent $files.append('%s.bw' % $counter) 475 #silent $files.append('%s.bw' % $counter)
476 #silent $labels.append("'%s'" % ($f.bigwig.display_name)) 476 #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name))
477 #end for 477 #end for
478 #end if 478 #end if
479 ]]> 479 ]]>
480 </token> 480 </token>
481 481