Mercurial > repos > bgruening > deeptools_plot_coverage

comparison deepTools_macros.xml @ 10:3317eb43a3c1 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0eeb2e1a184186ba5ac044136e71b943e2af0f09
author bgruening
date Mon, 05 Dec 2016 08:10:35 -0500
parents 71385153e5d5
children 4ae546bddd00
comparison
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9:71385153e5d5 10:3317eb43a3c1
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@">2.3.6</token> 101 <token name="@WRAPPER_VERSION@">2.4.1</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="2.3.6">deepTools</requirement> 105 <requirement type="package" version="2.4.1">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>
283 <option value="sum">sum</option> 283 <option value="sum">sum</option>
284 <option value="region_length">region length</option> 284 <option value="region_length">region length</option>
285 </param> 285 </param>
286 </xml> 286 </xml>
287 287
288 <xml name="sortRegionsComputeMatrix">
289 <param argument="--sortRegions" type="select" label="Sort regions"
290 help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
291 <option value="no">no ordering</option>
292 <option value="keep" selected="true">maintain the same ordering as the input files</option>
293 <option value="descend">descending order</option>
294 <option value="ascend">ascending order</option>
295 </param>
296 </xml>
297
288 <xml name="sortRegions"> 298 <xml name="sortRegions">
289 <param argument="--sortRegions" type="select" label="Sort regions" 299 <param argument="--sortRegions" type="select" label="Sort regions"
290 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.">
291 <option value="no">no ordering</option> 301 <option value="no">no ordering</option>
292 <option value="descend" selected="true">descending order</option> 302 <option value="descend">descending order</option>
293 <option value="ascend">ascending order</option> 303 <option value="ascend">ascending order</option>
294 </param> 304 </param>
295 </xml> 305 </xml>
296 306
297 <xml name="minMappingQuality"> 307 <xml name="minMappingQuality">
360 <yield /> 370 <yield />
361 </citations> 371 </citations>
362 </xml> 372 </xml>
363 373
364 <xml name="multiple_input_bams"> 374 <xml name="multiple_input_bams">
365 <param argument="--bamfiles" type="data" format="bam" min="1" 375 <conditional name="multibam_conditional">
366 label="Bam file" multiple="true" 376 <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.">
367 help=""/> 377 <option value="No" selected="true">No</option>
378 <option value="Yes">Yes</option>
379 </param>
380 <when value="No">
381 <param argument="--bamfiles" type="data" format="bam" min="1"
382 label="Bam file" multiple="true"
383 help=""/>
384 </when>
385 <when value="Yes">
386 <repeat name="multibam_repeats" min="1" title="BAM Files">
387 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
388 </repeat>
389 </when>
390 </conditional>
368 </xml> 391 </xml>
369 392
370 <xml name="multiple_input_bams_min2"> 393 <xml name="multiple_input_bams_min2">
371 <param argument="--bamfiles" type="data" format="bam" min="2" 394 <conditional name="multibam_conditional">
372 label="Bam file" multiple="true" 395 <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
373 help=""/> 396 is vital to you, select Yes below.">
397 <option value="No" selected="true">No</option>
398 <option value="Yes">Yes</option>
399 </param>
400 <when value="No">
401 <param argument="--bamfiles" type="data" format="bam" min="2"
402 label="Bam file" multiple="true"
403 help=""/>
404 </when>
405 <when value="Yes">
406 <repeat name="multibam_repeats" min="2" title="BAM Files">
407 <param argument="--bamfiles" type="data" format="bam" label="BAM file" help="" />
408 </repeat>
409 </when>
410 </conditional>
374 </xml> 411 </xml>
375 412
376 <xml name="multiple_input_bigwigs"> 413 <xml name="multiple_input_bigwigs">
377 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2" 414 <conditional name="multibigwig_conditional">
378 label="Bigwig file" 415 <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
379 help="A Bigwig file."/> 416 is vital to you, select Yes below.">
417 <option value="No" selected="true">No</option>
418 <option value="Yes">Yes</option>
419 </param>
420 <when value="No">
421 <param argument="--bigwigfiles" type="data" format="bigwig" multiple="True" min="2"
422 label="Bigwig file"
423 help="A Bigwig file."/>
424 </when>
425 <when value="Yes">
426 <repeat name="multibigwig_repeats" min="2" title="BigWig files">
427 <param argument="--bigwigfiles" type="data" format="bigwig" label="Bigwig file" help="A Bigwig file."/>
428 </repeat>
429 </when>
430 </conditional>
380 </xml> 431 </xml>
381 432
382 <xml name="plotTitle"> 433 <xml name="plotTitle">
383 <param argument="--plotTitle" type="text" value="" size="30" optional="True" 434 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
384 label="Title of the plot" 435 label="Title of the plot"
388 439
389 <token name="@multiple_input_bams@"> 440 <token name="@multiple_input_bams@">
390 <![CDATA[ 441 <![CDATA[
391 #set files=[] 442 #set files=[]
392 #set labels=[] 443 #set labels=[]
393 #for $counter, $bamfile in enumerate($bamfiles): 444 #if $multibam_conditional.orderMatters == "No":
394 ln -s "${bamfile}" "./${counter}.bam" && 445 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
395 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" && 446 ln -s "${bamfile}" "./${counter}.bam" &&
396 #silent $files.append('%s.bam' % $counter) 447 ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
397 #silent $labels.append("'%s'" % ($bamfile.display_name)) 448 #silent $files.append('%s.bam' % $counter)
398 #end for 449 #silent $labels.append("'%s'" % ($bamfile.display_name))
450 #end for
451 #else:
452 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
453 ln -s "${f.bamfile}" "./${counter}.bam" &&
454 ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
455 #silent $files.append('%s.bam' % $counter)
456 #silent $labels.append("'%s'" % ($f.bamfile.display_name))
457 #end for
458 #end if
399 ]]> 459 ]]>
400 </token> 460 </token>
401 461
402 <token name="@multiple_input_bigwigs@"> 462 <token name="@multiple_input_bigwigs@">
403 <![CDATA[ 463 <![CDATA[
404 #set files=[] 464 #set files=[]
405 #set labels=[] 465 #set labels=[]
406 #for $counter, $bigwig in enumerate($bigwigfiles): 466 #if $multibigwig_conditional.orderMatters == "No":
407 ln -s "${bigwig}" "${counter}.bw" && 467 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
408 #silent $files.append('%s.bw' % $counter) 468 ln -s "${bigwig}" "${counter}.bw" &&
409 #silent $labels.append("'%s'" % ($bigwig.display_name)) 469 #silent $files.append('%s.bw' % $counter)
410 #end for 470 #silent $labels.append("'%s'" % ($bigwig.display_name))
471 #end for
472 #else:
473 #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
474 ln -s "${f.bigwig}" "${counter}.bw" &&
475 #silent $files.append('%s.bw' % $counter)
476 #silent $labels.append("'%s'" % ($f.bigwig.display_name))
477 #end for
478 #end if
411 ]]> 479 ]]>
412 </token> 480 </token>
413 481
414 <xml name="blacklist"> 482 <xml name="blacklist">
415 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0" 483 <param argument="--blackListFileName" type="data" format="bed,gtf" multiple="true" optional="true" min="0"