Mercurial > repos > bgruening > deeptools_compute_matrix

comparison deepTools_macros.xml @ 27:459189886f08 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289
author bgruening
date Fri, 31 Mar 2017 08:26:05 -0400
parents 74eb6fd0b2d6
children 2f7094a2cfd5
comparison
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26:74eb6fd0b2d6 27:459189886f08
1 <macros> 1 <macros>
2
3 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
4 <token name="@WRAPPER_VERSION@">2.5.0</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="2.7.10">python</requirement>
8 <requirement type="package" version="@WRAPPER_VERSION@">deeptools</requirement>
9 <yield />
10 </requirements>
11 <expand macro="stdio" />
12 <version_command>@BINARY@ --version</version_command>
13 </xml>
2 14
3 <xml name="advancedOpt_scaffold"> 15 <xml name="advancedOpt_scaffold">
4 <conditional name="advancedOpt"> 16 <conditional name="advancedOpt">
5 <param name="showAdvancedOpt" type="select" label="Show advanced options" > 17 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
6 <option value="no" selected="true">no</option> 18 <option value="no" selected="true">no</option>
93 <add value="|"/> 105 <add value="|"/>
94 <add value=":"/> 106 <add value=":"/>
95 </valid> 107 </valid>
96 </sanitizer> 108 </sanitizer>
97 </param> 109 </param>
98 </xml>
99
100 <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
101 <token name="@WRAPPER_VERSION@">2.4.2</token>
102 <xml name="requirements">
103 <requirements>
104 <requirement type="package" version="2.7.10">python</requirement>
105 <requirement type="package" version="2.4.2">deeptools</requirement>
106 <yield />
107 </requirements>
108 <expand macro="stdio" />
109 <version_command>@BINARY@ --version</version_command>
110 </xml> 110 </xml>
111 111
112 <xml name="smoothLength"> 112 <xml name="smoothLength">
113 <param argument="--smoothLength" type="integer" value="" optional="True" min="1" 113 <param argument="--smoothLength" type="integer" value="" optional="True" min="1"
114 label="Smooth values using the following length (in bases)" 114 label="Smooth values using the following length (in bases)"
179 </xml> 179 </xml>
180 180
181 <xml name="fragLength"> 181 <xml name="fragLength">
182 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0" 182 <param argument="--minFragmentLength" type="integer" optional="True" value="0" min="0"
183 label="Minimum fragment length for inclusion." 183 label="Minimum fragment length for inclusion."
184 help="A value greater than 0 will filter out ALL single-end reads. This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." /> 184 help="This is primarily useful in things like ATACseq, where one would like to look specifically at mono- or di-nucleosome fragments." />
185 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0" 185 <param argument="--maxFragmentLength" type="integer" optional="True" value="0" min="0"
186 label="Maximum fragment length for inclusion." 186 label="Maximum fragment length for inclusion."
187 help="As above, but the maximum length. A value of 0 (the default) is equivalent to no maximum." /> 187 help="A value of 0 (the default) is equivalent to no maximum." />
188 </xml> 188 </xml>
189 189
190 <xml name="read_processing_options"> 190 <xml name="read_processing_options">
191 <expand macro="extendReads" /> 191 <expand macro="extendReads" />
192 <expand macro="ignoreDuplicates" /> 192 <expand macro="ignoreDuplicates" />
322 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/> 322 help ="If paired-end reads are used, the fragment length is computed from the BAM file, so this is only needed for single-end data."/>
323 </xml> 323 </xml>
324 324
325 <xml name="scaleFactor"> 325 <xml name="scaleFactor">
326 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor" 326 <param argument="--scaleFactor" type="float" value="1" label="Scaling factor"
327 help="When used in combination with --normalizeTo1x or 327 help="The computed scaling factor will be multiplied by this (default 1)." />
328 --normalizeUsingRPKM, the computed scaling factor will
329 be multiplied by the given scale factor." />
330 </xml> 328 </xml>
331 329
332 <xml name="scaleFactors"> 330 <xml name="scaleFactors">
333 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/> 331 <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment" help="(--scaleFactors)"/>
334 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/> 332 <param name="scaleFactor2" type="float" value="1" label="Scale factor for input" help="(--scaleFactors)"/>
439 437
440 <token name="@multiple_input_bams@"> 438 <token name="@multiple_input_bams@">
441 <![CDATA[ 439 <![CDATA[
442 #set files=[] 440 #set files=[]
443 #set labels=[] 441 #set labels=[]
442 #import re
444 #if $multibam_conditional.orderMatters == "No": 443 #if $multibam_conditional.orderMatters == "No":
445 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): 444 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
445 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier))
446 ln -s "${bamfile}" "./${counter}.bam" && 446 ln -s "${bamfile}" "./${counter}.bam" &&
447 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && 447 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
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'" % identifier)
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 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
453 ln -s "${f.bamfiles}" "./${counter}.bam" && 454 ln -s "${f.bamfiles}" "./${counter}.bam" &&
454 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" && 455 ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
455 #silent $files.append('%s.bam' % $counter) 456 #silent $files.append('%s.bam' % $counter)
456 #silent $labels.append("'%s'" % ($f.bamfiles.display_name)) 457 #silent $labels.append("'%s'" % $identifier)
457 #end for 458 #end for
458 #end if 459 #end if
459 ]]> 460 ]]>
460 </token> 461 </token>
461 462
462 <token name="@multiple_input_bigwigs@"> 463 <token name="@multiple_input_bigwigs@">
463 <![CDATA[ 464 <![CDATA[
464 #set files=[] 465 #set files=[]
465 #set labels=[] 466 #set labels=[]
467 #import re
466 #if $multibigwig_conditional.orderMatters == "No": 468 #if $multibigwig_conditional.orderMatters == "No":
467 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): 469 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
470 #set identifier = re.sub('[^\.\s\w\-]', '_', str($bigwig.element_identifier))
468 ln -s "${bigwig}" "${counter}.bw" && 471 ln -s "${bigwig}" "${counter}.bw" &&
469 #silent $files.append('%s.bw' % $counter) 472 #silent $files.append('%s.bw' % $counter)
470 #silent $labels.append("'%s'" % ($bigwig.display_name)) 473 #silent $labels.append("'%s'" % $identifier)
471 #end for 474 #end for
472 #else: 475 #else:
473 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats): 476 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
477 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
474 ln -s "${f.bigwigfiles}" "${counter}.bw" && 478 ln -s "${f.bigwigfiles}" "${counter}.bw" &&
475 #silent $files.append('%s.bw' % $counter) 479 #silent $files.append('%s.bw' % $counter)
476 #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name)) 480 #silent $labels.append("'%s'" % $identifier)
477 #end for 481 #end for
478 #end if 482 #end if
479 ]]> 483 ]]>
480 </token> 484 </token>
481 485