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"planemo upload commit 9e4d2776d6b3276e2849943439799b82d989bc3b"
author iuc
date Sun, 22 Dec 2019 17:11:12 +0000
parents 61f2dedb6b85
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43:61f2dedb6b85 44:03cec12dafc3
1 <tool id="multigps" name="MultiGPS" version="0.74.0"> 1 <tool id="multigps" name="MultiGPS" version="0.74.0">
2 <description>analyzes collections of multi-condition ChIP-seq data</description> 2 <description>analyzes collections of multi-condition ChIP-seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <expand macro="requirements" />
7 <requirement type="package" version="0.74">multigps</requirement>
8 </requirements>
9 <command detect_errors="aggressive"> 7 <command detect_errors="aggressive">
10 <![CDATA[ 8 <![CDATA[
11 #set output_dir = $output_html.files_path 9 #set output_dir = $output_html.files_path
12 mkdir -p $output_dir && 10 mkdir -p $output_dir &&
13 multigps 11 multigps
18 ## in the browser. 16 ## in the browser.
19 --eventsaretxt 17 --eventsaretxt
20 ## Do not run the parallel version of meme. 18 ## Do not run the parallel version of meme.
21 --meme1proc 19 --meme1proc
22 --threads \${GALAXY_SLOTS:-4} 20 --threads \${GALAXY_SLOTS:-4}
23 --geninfo '$chromInfo' 21 #if str($in_test_mode) == "no":
22 --geninfo '$chromInfo'
23 #else:
24 --geninfo '$__tool_directory__/tool-data/hg19.len'
25 #end if
24 ## Advanced options 26 ## Advanced options
25 #set aoc = $advanced_options_cond 27 #set aoc = $advanced_options_cond
26 #if str($aoc.advanced_options) == 'display': 28 #if str($aoc.advanced_options) == 'display':
27 #set bmsc = $aoc.binding_model_smoothing_cond 29 #set bmsc = $aoc.binding_model_smoothing_cond
28 #set gmsc = $aoc.gauss_model_smoothing_cond 30 #set gmsc = $aoc.gauss_model_smoothing_cond
408 </when> 410 </when>
409 </conditional> 411 </conditional>
410 </when> 412 </when>
411 <when value="hide" /> 413 <when value="hide" />
412 </conditional> 414 </conditional>
415 <!-- Functional testing -->
416 <param name="in_test_mode" type="hidden" value="no" />
413 </inputs> 417 </inputs>
414 <outputs> 418 <outputs>
415 <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}"> 419 <data name="output_design_file" format="tabular" label="${tool.name} (design file) on ${on_string}">
416 <filter>save_design_file == 'yes'</filter> 420 <filter>save_design_file == 'yes'</filter>
417 </data> 421 </data>
426 <repeat name="signal_repeat"> 430 <repeat name="signal_repeat">
427 <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" /> 431 <param name="signal" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
428 </repeat> 432 </repeat>
429 </repeat> 433 </repeat>
430 <param name="advanced_options" value="hide" /> 434 <param name="advanced_options" value="hide" />
435 <param name="in_test_mode" value="yes" />
431 <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/> 436 <output name="output_html" file="hg19_output_html1.html" ftype="html" compare="contains"/>
432 <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/> 437 <output name="output_bed" file="hg19_output_bed1.bed" ftype="bed"/>
433 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/> 438 <output name="all_events_table" file="hg19_all_events_table1.tabular" ftype="tabular"/>
434 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/> 439 <output name="replicates_counts" file="hg19_replicates_counts1.tabular" ftype="tabular"/>
435 </test> 440 </test>
441 <repeat name="control_repeat"> 446 <repeat name="control_repeat">
442 <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" /> 447 <param name="control" value="cntrl_hg19.scidx" ftype="scidx" dbkey="hg19" />
443 </repeat> 448 </repeat>
444 </repeat> 449 </repeat>
445 <param name="advanced_options" value="display" /> 450 <param name="advanced_options" value="display" />
451 <param name="in_test_mode" value="yes" />
446 <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/> 452 <output name="output_html" file="hg19_output_html2.html" ftype="html" compare="contains"/>
447 <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/> 453 <output name="output_bed" file="hg19_output_bed2.bed" ftype="bed"/>
448 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/> 454 <output name="all_events_table" file="hg19_all_events_table2.tabular" ftype="tabular"/>
449 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/> 455 <output name="replicates_counts" file="hg19_replicates_counts2.tabular" ftype="tabular"/>
450 </test> 456 </test>
464 470
465 **Options** 471 **Options**
466 472
467 * **Loading data:** 473 * **Loading data:**
468 474
469 - **Optional file containing reads from a control experiment** - must be same format as input experiment 475 - **Optional file containing reads from a control experiment** - file containing reads from a control experiment
470 - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model). 476 - **Fixed per-base limit** - Fixed per-base limit (default: estimated from background model).
471 - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be. 477 - **Poisson threshold for filtering per base** - Look at neighboring positions to decide what the per-base limit should be.
472 - **Use non-unique reads** - Use non-unique reads. 478 - **Use non-unique reads** - Use non-unique reads.
473 - **Fraction of the genome that is mappable for these experiments** - Fraction of the genome that is mappable for these experiments 479 - **Fraction of the genome that is mappable for these experiments** - Fraction of the genome that is mappable for these experiments
474 - **Turn off caching of the entire set of experiments?** - Flag to turn off caching of the entire set of experiments (i.e. run slower with less memory). 480 - **Turn off caching of the entire set of experiments?** - Flag to turn off caching of the entire set of experiments (i.e. run slower with less memory).
518 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value. 524 - **EdgeR over-dispersion parameter value** - EdgeR over-dispersion parameter value.
519 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment. 525 - **Minimum p-value for reporting differential enrichment** - Minimum p-value for reporting differential enrichment.
520 526
521 </help> 527 </help>
522 <citations> 528 <citations>
523 <citation type="bibtex"> 529 <citation type="doi">10.1371/journal.pcbi.1003501</citation>
524 @article{Mahony2014,
525 journal = {PLOS Computational Biology},
526 author = {1. Mahony S, Edwards MD, Mazzoni EO, Sherwood RI, Kakumanu A, Morrison CA, Wichterle H, Gifford DK},
527 title = {An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding},
528 year = {2014},}
529 volume = {10},
530 number = {3},
531 pages = {e1003501},}
532 </citation>
533 <citation type="bibtex">
534 @article{Liang2012,
535 journal = {BMC Bioinformatics},
536 author = {2. Liang, Ketes},
537 title = {Normalization of ChIP-seq data with control},
538 year = {2012},}
539 </citation>
540 </citations> 530 </citations>
541 </tool> 531 </tool>
542 532