Mercurial > repos > bgruening > deeptools_bam_pe_fragmentsize

comparison deepTools_macros.xml @ 28:7c1beb6d6eca draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit e7e3025eb4fffe5deb34c12a6d402d79241d9ed5
author bgruening
date Thu, 18 May 2023 20:41:10 +0000
parents 3f9dc453c0e8
children 195e98217334
comparison
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27:3f9dc453c0e8 28:7c1beb6d6eca
366 </xml> 366 </xml>
367 367
368 <xml name="pseudocount"> 368 <xml name="pseudocount">
369 <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/> 369 <param argument="--pseudocount" type="text" value="1 1" label="Pseudocount" help="Small number to avoid dividing by zero. You can specify separate values for the pseudocount added to the numerator and denominator by providing two values separated by a space."/>
370 </xml> 370 </xml>
371
372 <token name="@REFERENCES@"> 371 <token name="@REFERENCES@">
373 372
374 .. class:: infomark 373 .. class:: infomark
375 374
376 For more information on the tools, please visit our `help site`_. 375 For more information on the tools, please visit our `help site`_.
481 480
482 481
483 <token name="@multiple_input_bams@"> 482 <token name="@multiple_input_bams@">
484 <![CDATA[ 483 <![CDATA[
485 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": 484 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
486 #set custom_labels=labels 485 #set custom_labels=$custom_sample_labels_conditional.labels
487 #end if 486 #end if
488 #set files=[] 487 #set files=[]
489 #set labels=[] 488 #set labels=[]
490 #import re 489 #import re
491 #if $multibam_conditional.orderMatters == "No": 490 #if $multibam_conditional.orderMatters == "No":
496 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && 495 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
497 #else: 496 #else:
498 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && 497 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
499 #end if 498 #end if
500 #silent $files.append("'%s.bam'" % $counter) 499 #silent $files.append("'%s.bam'" % $counter)
501 #silent $labels.append("'%s'" % identifier) 500 #silent $labels.append("'%s'" % $identifier)
502 #end for 501 #end for
503 #else: 502 #else:
504 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): 503 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
505 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) 504 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
506 ln -s '${f.bamfiles}' './${counter}.bam' && 505 ln -s '${f.bamfiles}' './${counter}.bam' &&
520 </token> 519 </token>
521 520
522 <token name="@multiple_input_bigwigs@"> 521 <token name="@multiple_input_bigwigs@">
523 <![CDATA[ 522 <![CDATA[
524 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": 523 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
525 #set custom_labels=labels 524 #set custom_labels=$custom_sample_labels_conditional.labels
526 #end if 525 #end if
527 #set files=[] 526 #set files=[]
528 #set labels=[] 527 #set labels=[]
529 #import re 528 #import re
530 #if $multibigwig_conditional.orderMatters == "No": 529 #if $multibigwig_conditional.orderMatters == "No":