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comparison rg_rnaStar.xml @ 9:0a563fd2f22e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
author iuc
date Thu, 14 Mar 2019 16:12:38 -0400
parents d5659efd66aa
children d82339e37e8e
comparison
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8:d5659efd66aa 9:0a563fd2f22e
1 <tool id="rna_star" name="RNA STAR" version="2.6.0b-1" profile="17.01"> 1 <tool id="rna_star" name="RNA STAR" version="2.6.0b-2" profile="17.01">
2 <description>Gapped-read mapper for RNA-seq data</description> 2 <description>Gapped-read mapper for RNA-seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 7
8 <stdio> 8 <stdio>
9 <regex match="FATAL error" source="both" level="fatal"/> 9 <regex match="FATAL error" source="both" level="fatal"/>
10 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/> 10 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
11 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/> 11 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
12 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/> 12 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
141 --seedSearchLmax "$params.seed.seedSearchLmax" 141 --seedSearchLmax "$params.seed.seedSearchLmax"
142 --seedMultimapNmax "$params.seed.seedMultimapNmax" 142 --seedMultimapNmax "$params.seed.seedMultimapNmax"
143 --seedPerReadNmax "$params.seed.seedPerReadNmax" 143 --seedPerReadNmax "$params.seed.seedPerReadNmax"
144 --seedPerWindowNmax "$params.seed.seedPerWindowNmax" 144 --seedPerWindowNmax "$params.seed.seedPerWindowNmax"
145 --seedNoneLociPerWindow "$params.seed.seedNoneLociPerWindow" 145 --seedNoneLociPerWindow "$params.seed.seedNoneLociPerWindow"
146 146
147 ## Alignment parameter options 147 ## Alignment parameter options
148 --alignIntronMin "$params.align.alignIntronMin" 148 --alignIntronMin "$params.align.alignIntronMin"
149 --alignIntronMax "$params.align.alignIntronMax" 149 --alignIntronMax "$params.align.alignIntronMax"
150 --alignMatesGapMax "$params.align.alignMatesGapMax" 150 --alignMatesGapMax "$params.align.alignMatesGapMax"
151 --alignSJoverhangMin "$params.align.alignSJoverhangMin" 151 --alignSJoverhangMin "$params.align.alignSJoverhangMin"
159 159
160 ## Two pass mode 160 ## Two pass mode
161 --twopassMode "$params.twopass.twopassMode" 161 --twopassMode "$params.twopass.twopassMode"
162 #if str( $params.twopass.twopassMode ) == "Basic": 162 #if str( $params.twopass.twopassMode ) == "Basic":
163 --twopass1readsN "$params.twopass.twopass1readsN" 163 --twopass1readsN "$params.twopass.twopass1readsN"
164 #if not $refGenomeSource.sjdbGTFfile:
165 --sjdbOverhang '$refGenomeSource.sjdbOverhang'
166 #end if
164 #end if 167 #end if
165 168
166 ## Chimeric alignment parameter options 169 ## Chimeric alignment parameter options
167 #if str( $params.chim.chim_select ) == "yes": 170 #if str( $params.chim.chim_select ) == "yes":
168 --chimOutType Junctions SeparateSAMold 171 --chimOutType Junctions SeparateSAMold
239 <filter type="static_value" column="4" value="0"/> 242 <filter type="static_value" column="4" value="0"/>
240 <filter type="sort_by" column="2" /> 243 <filter type="sort_by" column="2" />
241 <validator type="no_options" message="No indexes are available for the selected input dataset"/> 244 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
242 </options> 245 </options>
243 </param> 246 </param>
244 247
245 <expand macro="@SJDBOPTIONS@" /> 248 <expand macro="@SJDBOPTIONS@" />
246 </when> 249 </when>
247 </conditional> 250 </conditional>
248 </when> 251 </when>
249 <when value="history"> 252 <when value="history">
276 </param> 279 </param>
277 <param argument="--outFilterIntronStrands" type="select" label="Filter alignments containing junctions with inconsistent strands"> 280 <param argument="--outFilterIntronStrands" type="select" label="Filter alignments containing junctions with inconsistent strands">
278 <option value="RemoveInconsistentStrands" selected="true">Remove alignments that have junctions with inconsistent strands</option> 281 <option value="RemoveInconsistentStrands" selected="true">Remove alignments that have junctions with inconsistent strands</option>
279 <option value="None">No filtering</option> 282 <option value="None">No filtering</option>
280 </param> 283 </param>
281 284
282 <!-- Additional output parameter settings. --> 285 <!-- Additional output parameter settings. -->
283 <conditional name="output_params2"> 286 <conditional name="output_params2">
284 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?"> 287 <param name="output_select2" type="select" label="Would you like to set additional output parameters (formatting and filtering)?">
285 <option value="no" selected="true">No</option> 288 <option value="no" selected="true">No</option>
286 <option value="yes">Yes</option> 289 <option value="yes">Yes</option>
319 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option> 322 <option value="star_fusion">Use parameters suggested for STAR-Fusion</option>
320 <option value="full">Extended parameter list</option> 323 <option value="full">Extended parameter list</option>
321 </param> 324 </param>
322 <when value="default"/> 325 <when value="default"/>
323 <when value="star_fusion"/><!-- Set STAR-fusion parameters automatically --> 326 <when value="star_fusion"/><!-- Set STAR-fusion parameters automatically -->
324 327
325 <when value="full"> 328 <when value="full">
326 <section name="seed" title="Seed parameters" expanded="False"> 329 <section name="seed" title="Seed parameters" expanded="False">
327 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/> 330 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
328 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/> 331 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/>
329 <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/> 332 <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/>
330 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/> 333 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
331 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/> 334 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
332 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/> 335 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
333 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/> 336 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
334 </section> 337 </section>
335 338
336 <section name="align" title="Alignment parameters" expanded="False"> 339 <section name="align" title="Alignment parameters" expanded="False">
337 <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/> 340 <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
338 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/> 341 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
339 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/> 342 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
340 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/> 343 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
356 <param argument="--limitBAMsortRAM" type="integer" min="0" value="0" label="Maximum available RAM (in bytes) for sorting" help="If 0, this will be set to the genome index size. This is typically only changed in cases where an error is produced." /> 359 <param argument="--limitBAMsortRAM" type="integer" min="0" value="0" label="Maximum available RAM (in bytes) for sorting" help="If 0, this will be set to the genome index size. This is typically only changed in cases where an error is produced." />
357 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" /> 360 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
358 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" /> 361 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
359 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." /> 362 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
360 </section> 363 </section>
361 364
362 <conditional name="chim"> 365 <conditional name="chim">
363 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?"> 366 <param name="chim_select" type="select" label="Would you like to set chimeric alignment parameters?">
364 <option value="no" selected="true">No</option> 367 <option value="no" selected="true">No</option>
365 <option value="yes">Yes</option> 368 <option value="yes">Yes</option>
366 </param> 369 </param>
402 </data> 405 </data>
403 406
404 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="Aligned.sortedByCoord.out.bam"> 407 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam" from_work_dir="Aligned.sortedByCoord.out.bam">
405 <expand macro="dbKeyActions" /> 408 <expand macro="dbKeyActions" />
406 </data> 409 </data>
407 410
408 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab"> 411 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
409 <filter>quantMode is True</filter> 412 <filter>quantMode is True</filter>
410 <expand macro="dbKeyActions" /> 413 <expand macro="dbKeyActions" />
411 </data> 414 </data>
412 </outputs> 415 </outputs>
420 423
421 <param name="output_select" value="yes" /> 424 <param name="output_select" value="yes" />
422 <param name="outSAMattributes" value="All" /> 425 <param name="outSAMattributes" value="All" />
423 <param name="outSAMstrandField" value="intronMotif" /> 426 <param name="outSAMstrandField" value="intronMotif" />
424 <param name="settingsType" value="default" /> 427 <param name="settingsType" value="default" />
425 428
426 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/> 429 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
427 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> 430 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
428 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> 431 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
429 </test> 432 </test>
430 <test><!-- tests gtf file and GeneCounts mode --> 433 <test><!-- tests gtf file and GeneCounts mode -->
439 <param name="sPaired" value="single" /> 442 <param name="sPaired" value="single" />
440 <param name="output_select" value="yes" /> 443 <param name="output_select" value="yes" />
441 <param name="outSAMattributes" value="All" /> 444 <param name="outSAMattributes" value="All" />
442 <param name="outSAMstrandField" value="intronMotif" /> 445 <param name="outSAMstrandField" value="intronMotif" />
443 <param name="settingsType" value="default" /> 446 <param name="settingsType" value="default" />
444 447
445 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/> 448 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
446 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> 449 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
447 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> 450 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
448 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" /> 451 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" />
449 </test> 452 </test>
450 <test> 453 <test>
451 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> 454 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
452 <param name="geneSource" value="history" /> 455 <param name="geneSource" value="history" />
453 <param name="genomeFastaFiles" value="tophat_test.fa" /> 456 <param name="genomeFastaFiles" value="tophat_test.fa" />
454 <param name="sPaired" value="single" /> 457 <param name="sPaired" value="single" />
455 458
456 <param name="output_select" value="yes" /> 459 <param name="output_select" value="yes" />
457 <param name="outSAMattributes" value="All" /> 460 <param name="outSAMattributes" value="All" />
458 <param name="outSAMstrandField" value="intronMotif" /> 461 <param name="outSAMstrandField" value="intronMotif" />
459 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" /> 462 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
460 463
461 <param name="output_select2" value="yes" /> 464 <param name="output_select2" value="yes" />
462 <param name="outFilterScoreMinOverLread" value="0.9" /> 465 <param name="outFilterScoreMinOverLread" value="0.9" />
463 <param name="settingsType" value="full" /> 466 <param name="settingsType" value="full" />
464 <param name="seed_select" value="yes" /> 467 <param name="seed_select" value="yes" />
465 <param name="seedSearchStartLmax" value="25" /> 468 <param name="seedSearchStartLmax" value="25" />
506 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" /> 509 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
507 510
508 <param name="output_select2" value="yes" /> 511 <param name="output_select2" value="yes" />
509 <param name="settingsType" value="full" /> 512 <param name="settingsType" value="full" />
510 <param name="chim_select" value="false" /> 513 <param name="chim_select" value="false" />
511 514
512 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/> 515 <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="12"/>
513 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> 516 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
517 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
518 </test>
519 <test>
520 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
521 <param name="geneSource" value="history" />
522 <param name="genomeFastaFiles" value="tophat_test.fa" />
523 <param name="sPaired" value="single" />
524
525 <param name="output_select" value="yes" />
526 <param name="outSAMattributes" value="All" />
527 <param name="outSAMstrandField" value="intronMotif" />
528 <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />
529
530 <param name="output_select2" value="yes" />
531 <param name="settingsType" value="full" />
532 <param name="twopass" value="true" />
533 <param name="twopassMode" value="Basic" />
534 <param name="chim_select" value="false" />
535
536 <output name="output_log" file="rnastar_test_twopass.log" compare="diff" lines_diff="12"/>
537 <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>
514 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> 538 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
515 </test> 539 </test>
516 </tests> 540 </tests>
517 <help> 541 <help>
518 **What it does** 542 **What it does**
548 "STAR: ultrafast universal RNA-seq aligner" 572 "STAR: ultrafast universal RNA-seq aligner"
549 A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635 573 A. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635
550 574
551 Galaxy_ (that's what you are using right now!) for gluing everything together 575 Galaxy_ (that's what you are using right now!) for gluing everything together
552 576
553 Most of the work for this wrapper XML is Jeremy Goecks' original STAR_ wrapper 577 Most of the work for this wrapper XML is Jeremy Goecks' original STAR wrapper
554 578
555 Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies 579 Minor tweaks to output names to suit our downstream purposes, toolshed automated dependencies
556 and odds and ends of other code and documentation comprising this tool was 580 and odds and ends of other code and documentation comprising this tool was
557 written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts 581 written by Ross Lazarus and that part is licensed_ the same way as other rgenetics artefacts
558 582
559 .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml
560 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/ 583 .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/
561 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion 584 .. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion
562 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs 585 .. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs
563 .. _rna_star: https://github.com/alexdobin/STAR 586 .. _rna_star: https://github.com/alexdobin/STAR
564 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full 587 .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full