Mercurial > repos > bgruening > deeptools_bam_coverage

comparison deepTools_macros.xml @ 42:0d2ba04b8261 draft default tip

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
author bgruening
date Thu, 01 Jun 2023 10:23:48 +0000
parents a4ecef241a6d
children
comparison
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41:a4ecef241a6d 42:0d2ba04b8261
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@">3.5.1.0</token> 4 <token name="@TOOL_VERSION@">3.5.2</token>
5 <token name="@GALAXY_VERSION@">20.01</token>
5 <xml name="requirements"> 6 <xml name="requirements">
6 <requirements> 7 <requirements>
7 <requirement type="package" version="3.5.1">deeptools</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">deeptools</requirement>
8 <requirement type="package" version="1.9">samtools</requirement> 9 <requirement type="package" version="1.9">samtools</requirement>
9 </requirements> 10 </requirements>
10 <expand macro="stdio" /> 11 <expand macro="stdio" />
11 <version_command>@BINARY@ --version</version_command> 12 <version_command>@BINARY@ --version</version_command>
12 </xml> 13 </xml>
366 </xml> 367 </xml>
367 368
368 <xml name="pseudocount"> 369 <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."/> 370 <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> 371 </xml>
371
372 <token name="@REFERENCES@"> 372 <token name="@REFERENCES@">
373 373
374 .. class:: infomark 374 .. class:: infomark
375 375
376 For more information on the tools, please visit our `help site`_. 376 For more information on the tools, please visit our `help site`_.
481 481
482 482
483 <token name="@multiple_input_bams@"> 483 <token name="@multiple_input_bams@">
484 <![CDATA[ 484 <![CDATA[
485 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": 485 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
486 #set custom_labels=labels 486 #set custom_labels=$custom_sample_labels_conditional.labels
487 #end if 487 #end if
488 #set files=[] 488 #set files=[]
489 #set labels=[] 489 #set labels=[]
490 #import re 490 #import re
491 #if $multibam_conditional.orderMatters == "No": 491 #if $multibam_conditional.orderMatters == "No":
496 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && 496 ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' &&
497 #else: 497 #else:
498 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && 498 ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' &&
499 #end if 499 #end if
500 #silent $files.append("'%s.bam'" % $counter) 500 #silent $files.append("'%s.bam'" % $counter)
501 #silent $labels.append("'%s'" % identifier) 501 #silent $labels.append("'%s'" % $identifier)
502 #end for 502 #end for
503 #else: 503 #else:
504 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): 504 #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
505 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) 505 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier))
506 ln -s '${f.bamfiles}' './${counter}.bam' && 506 ln -s '${f.bamfiles}' './${counter}.bam' &&
520 </token> 520 </token>
521 521
522 <token name="@multiple_input_bigwigs@"> 522 <token name="@multiple_input_bigwigs@">
523 <![CDATA[ 523 <![CDATA[
524 #if $custom_sample_labels_conditional.custom_labels_select == "Yes": 524 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
525 #set custom_labels=labels 525 #set custom_labels=$custom_sample_labels_conditional.labels
526 #end if 526 #end if
527 #set files=[] 527 #set files=[]
528 #set labels=[] 528 #set labels=[]
529 #import re 529 #import re
530 #if $multibigwig_conditional.orderMatters == "No": 530 #if $multibigwig_conditional.orderMatters == "No":