Mercurial > repos > iuc > rgrnastar
comparison rg_rnaStar.xml @ 9:0a563fd2f22e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 361e5d7743be86c2ba6c207836c0c5b75e071eb7
author | iuc |
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date | Thu, 14 Mar 2019 16:12:38 -0400 |
parents | d5659efd66aa |
children | d82339e37e8e |
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8:d5659efd66aa | 9:0a563fd2f22e |
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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 |