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comparison deepTools_macros.xml @ 22:59cbb059cd1e draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 6507b14607984c6f48d9866922a17132de4bb54d
author bgruening
date Tue, 19 Feb 2019 10:03:16 -0500
parents e4287c038599
children c09c23eaf116
comparison
equal deleted inserted replaced
21:e4287c038599 22:59cbb059cd1e
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@">3.1.2.0</token> 4 <token name="@WRAPPER_VERSION@">3.2.0.0</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="3.1.2">deeptools</requirement> 7 <requirement type="package" version="3.2.0">deeptools</requirement>
8 <requirement type="package" version="1.7">samtools</requirement> 8 <requirement type="package" version="1.9">samtools</requirement>
9 </requirements> 9 </requirements>
10 <expand macro="stdio" /> 10 <expand macro="stdio" />
11 <version_command>@BINARY@ --version</version_command> 11 <version_command>@BINARY@ --version</version_command>
12 </xml> 12 </xml>
13 13
357 <regex match="Traceback" /> 357 <regex match="Traceback" />
358 </stdio> 358 </stdio>
359 </xml> 359 </xml>
360 360
361 <xml name="pseudocount"> 361 <xml name="pseudocount">
362 <param argument="--pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/> 362 <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."/>
363 </xml> 363 </xml>
364 364
365 <token name="@REFERENCES@"> 365 <token name="@REFERENCES@">
366 366
367 .. class:: infomark 367 .. class:: infomark
421 </repeat> 421 </repeat>
422 </when> 422 </when>
423 </conditional> 423 </conditional>
424 </xml> 424 </xml>
425 425
426 <xml name="custom_sample_labels">
427 <conditional name="custom_sample_labels_conditional">
428 <param name="custom_labels_select" type="select" label="Would you like custom sample labels?" help="By default, the names of the samples in your history are used.">
429 <option value="No" selected="true">No, use sample names in the history</option>
430 <option value="Yes">Yes, I want to specify new labels</option>
431 </param>
432 <when value="No">
433 </when>
434 <when value="Yes">
435 <param argument="--labels" type="text" label="Sample Labels" help="Labels, separated by a space. If your labels themselves contain spaces then please enclose them in quotes (e.g., &quot;sample 1&quot; &quot;sample 2&quot;)">
436 <sanitizer>
437 <valid initial="string.printable">
438 </valid>
439 </sanitizer>
440 </param>
441 </when>
442 </conditional>
443 </xml>
444
426 <xml name="plotTitle"> 445 <xml name="plotTitle">
427 <param argument="--plotTitle" type="text" value="" size="30" optional="True" 446 <param argument="--plotTitle" type="text" value="" size="30" optional="True"
428 label="Title of the plot" 447 label="Title of the plot"
429 help="Title of the plot, to be printed on top of the generated image." /> 448 help="Title of the plot, to be printed on top of the generated image." />
430 </xml> 449 </xml>
431 450
451 <xml name="legendLocation">
452 <param argument="--legendLocation" type="select" label="Legend location" help="Location for the legend in the summary plot. Note that none cannot be used in plotProfile.">
453 <option value="best" selected="true">Best (automatic)</option>
454 <option value="upper-right">upper-right</option>
455 <option value="upper-left">upper-left</option>
456 <option value="upper-center">upper-center</option>
457 <option value="lower-right">lower-right</option>
458 <option value="lower-left">lower-left</option>
459 <option value="lower-center">lower-center</option>
460 <option value="center-right">center-right</option>
461 <option value="center-left">center-left</option>
462 <option value="center">center</option>
463 <option value="none">none (only works for heatmaps</option>
464 </param>
465 </xml>
466
432 <xml name="labelRotation"> 467 <xml name="labelRotation">
433 <param argument="--labelRotation" type="integer" value="0" 468 <param argument="--labelRotation" type="integer" value="0"
434 label="Rotation of the X-axis labels (in degrees)" 469 label="Rotation of the X-axis labels (in degrees)"
435 help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." /> 470 help="The rotation of things like TSS or TES on the X-axis of profile plots in both plotHeatmap and plotProfile. The default is 0, positive values denome a counter-clockwise rotation." />
436 </xml> 471 </xml>
437 472
438 473
439 <token name="@multiple_input_bams@"> 474 <token name="@multiple_input_bams@">
440 <![CDATA[ 475 <![CDATA[
476 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
477 #set custom_labels=labels
478 #end if
441 #set files=[] 479 #set files=[]
442 #set labels=[] 480 #set labels=[]
443 #import re 481 #import re
444 #if $multibam_conditional.orderMatters == "No": 482 #if $multibam_conditional.orderMatters == "No":
445 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): 483 #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles):
464 #end if 502 #end if
465 #silent $files.append("'%s.bam'" % $counter) 503 #silent $files.append("'%s.bam'" % $counter)
466 #silent $labels.append("'%s'" % $identifier) 504 #silent $labels.append("'%s'" % $identifier)
467 #end for 505 #end for
468 #end if 506 #end if
507 #if $custom_sample_labels_conditional.custom_labels_select == "Yes":
508 #set labels=custom_labels
509 #end if
469 ]]> 510 ]]>
470 </token> 511 </token>
471 512
472 <token name="@multiple_input_bigwigs@"> 513 <token name="@multiple_input_bigwigs@">
473 <![CDATA[ 514 <![CDATA[
515 #if $custom_labels_conditional.custom_labels_select == "Yes":
516 #set custom_labels=labels
517 #end if
474 #set files=[] 518 #set files=[]
475 #set labels=[] 519 #set labels=[]
476 #import re 520 #import re
477 #if $multibigwig_conditional.orderMatters == "No": 521 #if $multibigwig_conditional.orderMatters == "No":
478 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles): 522 #for $counter, $bigwig in enumerate($multibigwig_conditional.bigwigfiles):
486 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier)) 530 #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bigwigfiles.element_identifier))
487 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' && 531 ln -f -s '${f.bigwigfiles}' '${identifier}_${counter}.bw' &&
488 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter)) 532 #silent $files.append("'%s_%s.bw'" % ($identifier, $counter))
489 #silent $labels.append("'%s'" % $identifier) 533 #silent $labels.append("'%s'" % $identifier)
490 #end for 534 #end for
535 #end if
536 #if $custom_labels_conditional.custom_labels_select == "Yes":
537 #set labels=custom_labels
491 #end if 538 #end if
492 ]]> 539 ]]>
493 </token> 540 </token>
494 541
495 <xml name="blacklist"> 542 <xml name="blacklist">