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comparison macros.xml @ 32:4746de55986e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit e5d0d8e40525840311dea1d212af911a6eade256
author iuc
date Sat, 31 May 2025 19:51:43 +0000
parents 9b7a86a83fce
children
comparison
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31:9b7a86a83fce 32:4746de55986e
2 <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@ 2 <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@
3 whenever you make changes to the @TOOL_VERSION@ token! 3 whenever you make changes to the @TOOL_VERSION@ token!
4 The data manager uses a symlink to this macro file to keep the STAR and 4 The data manager uses a symlink to this macro file to keep the STAR and
5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ --> 5 the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->
6 <!-- STAR version to be used --> 6 <!-- STAR version to be used -->
7 <token name="@TOOL_VERSION@">2.7.11a</token> 7 <token name="@TOOL_VERSION@">2.7.11b</token>
8 <token name="@VERSION_SUFFIX@">1</token> 8 <token name="@VERSION_SUFFIX@">0</token>
9 <token name="@PROFILE@">21.01</token> 9 <token name="@PROFILE@">21.01</token>
10 <!-- STAR index version compatible with this version of STAR 10 <!-- STAR index version compatible with this version of STAR
11 This is the STAR version that introduced the index structure expected 11 This is the STAR version that introduced the index structure expected
12 by the current version. 12 by the current version.
13 It can be found for any specific version of STAR with: 13 It can be found for any specific version of STAR with:
119 ## Diploid mode 119 ## Diploid mode
120 #if 'diploidconditional' in $refGenomeSource: 120 #if 'diploidconditional' in $refGenomeSource:
121 #if str($refGenomeSource.diploidconditional.diploid) == 'Yes': 121 #if str($refGenomeSource.diploidconditional.diploid) == 'Yes':
122 --genomeTransformVCF '${refGenomeSource.diploidconditional.genomeTransformVCF}' 122 --genomeTransformVCF '${refGenomeSource.diploidconditional.genomeTransformVCF}'
123 --genomeTransformType Diploid 123 --genomeTransformType Diploid
124 #end if 124 #end if
125 #end if 125 #end if
126 --runThreadN \${GALAXY_SLOTS:-4} 126 --runThreadN \${GALAXY_SLOTS:-4}
127 ## in bytes 127 ## in bytes
128 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000)) 128 --limitGenomeGenerateRAM \$((\${GALAXY_MEMORY_MB:-31000} * 1000000))
129 && 129 &&
369 <change_format> 369 <change_format>
370 <when input="outWig.outWigType" value="wiggle" format="wig"/> 370 <when input="outWig.outWigType" value="wiggle" format="wig"/>
371 </change_format> 371 </change_format>
372 </data> 372 </data>
373 </xml> 373 </xml>
374 <xml name="quantTranscriptomeSAMoutput_param">
375 <param argument="--quantTranscriptomeSAMoutput" type="select" label="Alignment filtering for TranscriptomeSAM output">
376 <option value="BanSingleEnd_BanIndels_ExtendSoftclip" selected="true">prohibit indels and single-end alignments, extend softclips - compatible with RSEM</option>
377 <option value="BanSingleEnd">prohibit single-end alignments, allow indels and softclips</option>
378 <option value="BanSingleEnd_ExtendSoftclip">prohibit single-end alignments, extend softclips, allow indels</option>
379 </param>
380 </xml>
374 <xml name="quantMode"> 381 <xml name="quantMode">
375 <conditional name="quantmode_output"> 382 <conditional name="quantmode_output">
376 <param argument="--quantMode" type="select" label="Per gene/transcript output" help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!"> 383 <param argument="--quantMode" type="select" label="Per gene/transcript output" help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">
377 <option value="-">No per gene or transcript output</option> 384 <option value="-">No per gene or transcript output</option>
378 <option value="GeneCounts">Per gene read counts (GeneCounts)</option> 385 <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
380 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option> 387 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
381 </param> 388 </param>
382 <when value="-"/> 389 <when value="-"/>
383 <when value="GeneCounts"/> 390 <when value="GeneCounts"/>
384 <when value="TranscriptomeSAM"> 391 <when value="TranscriptomeSAM">
385 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled."/> 392 <expand macro="quantTranscriptomeSAMoutput_param"/>
386 </when> 393 </when>
387 <when value="TranscriptomeSAM GeneCounts"> 394 <when value="TranscriptomeSAM GeneCounts">
388 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend" label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?" help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled."/> 395 <expand macro="quantTranscriptomeSAMoutput_param"/>
389 </when> 396 </when>
390 </conditional> 397 </conditional>
391 </xml> 398 </xml>
392 <xml name="quantModeNoGTF"> 399 <xml name="quantModeNoGTF">
393 <conditional name="quantmode_output"> 400 <conditional name="quantmode_output">
430 <param argument="--varVCFfile" type="data" format="vcf" label="VCF file with personal variants" help="Each variant is expected to have a genotype with two alleles. The VCF file needs to have the 10th column with genotype recorded as 0/1, 1/0, 1/1 (or | instead of /)"/> 437 <param argument="--varVCFfile" type="data" format="vcf" label="VCF file with personal variants" help="Each variant is expected to have a genotype with two alleles. The VCF file needs to have the 10th column with genotype recorded as 0/1, 1/0, 1/1 (or | instead of /)"/>
431 </when> 438 </when>
432 <when value=""/> 439 <when value=""/>
433 </conditional> 440 </conditional>
434 </xml> 441 </xml>
442 <xml name="full_algo_params">
443 <section name="seed" title="Seed parameters" expanded="false">
444 <param argument="--seedSearchStartLmax" type="integer" min="1" value="50" label="Search start point through the read"/>
445 <param argument="--seedSearchStartLmaxOverLread" type="float" min="0" value="1.0" label="Search start point through the read, normalized to read length"/>
446 <param argument="--seedSearchLmax" type="integer" min="0" value="0" label="Maximum length of seeds" help="Default of 0 indicates no maximum length"/>
447 <param argument="--seedMultimapNmax" type="integer" min="1" value="10000" label="Maximum number of mappings to use a piece in stitching"/>
448 <param argument="--seedPerReadNmax" type="integer" min="1" value="1000" label="Maximum number of seeds per read"/>
449 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
450 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
451 </section>
452 <section name="align" title="Alignment parameters" expanded="false">
453 <param argument="--alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
454 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
455 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
456 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
457 <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true">
458 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/>
459 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax2" type="integer" min="-1" value="-1" label="GT/AG and CT/AC motif"/>
460 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax3" type="integer" min="-1" value="0" label="GC/AG and CT/GC motif"/>
461 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax4" type="integer" min="-1" value="0" label="AT/AC and GT/AT motif"/>
462 </section>
463 <param argument="--alignSJDBoverhangMin" type="integer" min="1" value="3" label="Minimum overhang for annotated spliced alignments"/>
464 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
465 <param argument="--alignSplicedMateMapLminOverLmate" type="float" min="0" value="0.66" label="Minimum mapped length for a read mate that is spliced, normalized to mate length"/>
466 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
467 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
468 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
469 <param argument="--alignEndsType" type="select" label="type of read ends alignment">
470 <option value="Local">standard local alignment with soft-clipping allowed</option>
471 <option value="EndToEnd">force end-to-end read alignment, do not soft-clip</option>
472 <option value="Extend5pOfRead1">fully extend only the 5p of the read1, all other ends: local alignment</option>
473 <option value="Extend5pOfReads12">fully extend only the 5p of the both read1 and read2, all other ends: local alignment</option>
474 </param>
475 <param argument="--peOverlapNbasesMin" type="integer" min="0" value="0"
476 label="minimum number of overlap bases to trigger mates merging and realignment" />
477 <param argument="--peOverlapMMp" type="float" min="0" max="1" value="0.01"
478 label="maximum proportion of mismatched bases in the overlap area" />
479 </section>
480 <section name="chim_settings" title="Chimeric alignment parameters" expanded="false">
481 <param argument="--chimSegmentMin" type="integer" min="1" value="12"
482 label="Minimum length of chimeric segment"
483 help="For small numbers this will cause large number of chimeric alignments. A value of 12 is commonly used." />
484 <param argument="--chimScoreMin" type="integer" min="0" value="0"
485 label="Minimum total (summed) score of chimeric segments"/>
486 <param argument="--chimScoreDropMax" type="integer" min="0" value="20"
487 label="Maximum difference of chimeric score from read length"/>
488 <param argument="--chimScoreSeparation" type="integer" min="0" value="10"
489 label="Minimum difference between the best chimeric score and the next one"/>
490 <param argument="--chimScoreJunctionNonGTAG" type="integer" value="-1"
491 label="Penalty for a non-GT/AG chimeric junction"/>
492 <param argument="--chimJunctionOverhangMin" type="integer" min="0" value="20"
493 label="Minimum overhang for a chimeric junction"/>
494 <param argument="--chimSegmentReadGapMax" type="integer" min="0" value="0"
495 label="Maximum gap in the read sequence between chimeric segments" />
496 <param argument="--chimFilter" type="boolean" truevalue="banGenomicN" falsevalue="None" checked="true"
497 label="Discard chimeric alignments with Ns in the genome sequence around the chimeric junction" />
498 <param argument="--chimMainSegmentMultNmax" type="integer" min="1" value="10"
499 label="Maximum number of multi-alignments for the main chimeric segment."
500 help="A value of 1 prohibits multimapping main segments"/>
501 <param argument="--chimMultimapNmax" type="integer" min="1" value="1"
502 label="Maximum number of chimeric multi-alignments"
503 help="The default value of 1 only considers unique alignments. If you chose to report chimeric alignments alongside regular ones in the BAM output, this setting is ignored and only uniquely mapping chimeric reads get reported. " />
504 <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1"
505 label="Score range for multi-mapping chimeras"
506 help="The threshold below the best chimeric score that a multimapping chimera must have to be output. This is ignored unless --chimMultimapNmax is above 1" />
507 </section>
508 <expand macro="limits" />
509 </xml>
510 <xml name="chim_params">
511 <param argument="--chimOutType" type="select"
512 label="Report chimeric alignments?"
513 help="Choose if and how chimeric alignments should be reported. STAR-Fusion users should select the 'Junctions' option and use the resulting tabular dataset as input to STAR-Fusion. Everyone else: note that selecting 'WithinBAM' or 'WithinBAM Junctions' disables the --chimMultimapNmax setting in the algorithmic parameters section below (the tool will only consider uniquely mapped reads in the search for chimeric alignments). If you disable the reporting of chimeric alignments here, then all chimeric alignment settings in the algorithmic parameters section below will be ignored.">
514 <option value="">Don't report chimeric alignments</option>
515 <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option>
516 <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>
517 <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option>
518 <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option>
519 </param>
520 </xml>
521 <token name="@ALGO_FULL@"><![CDATA[
522 ## Extended parameter options
523
524 ## Seed parameter options
525 --seedSearchStartLmax ${algo.params.seed.seedSearchStartLmax}
526 --seedSearchStartLmaxOverLread ${algo.params.seed.seedSearchStartLmaxOverLread}
527 --seedSearchLmax ${algo.params.seed.seedSearchLmax}
528 --seedMultimapNmax ${algo.params.seed.seedMultimapNmax}
529 --seedPerReadNmax ${algo.params.seed.seedPerReadNmax}
530 --seedPerWindowNmax ${algo.params.seed.seedPerWindowNmax}
531 --seedNoneLociPerWindow ${algo.params.seed.seedNoneLociPerWindow}
532
533 ## Alignment parameter options
534 --alignIntronMin ${algo.params.align.alignIntronMin}
535 --alignIntronMax ${algo.params.align.alignIntronMax}
536 --alignMatesGapMax ${algo.params.align.alignMatesGapMax}
537 --alignSJoverhangMin ${algo.params.align.alignSJoverhangMin}
538 --alignSJstitchMismatchNmax ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax1} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax2} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax3} ${algo.params.align.alignSJstitchMismatchNmax.alignSJstitchMismatchNmax4}
539 --alignSJDBoverhangMin ${algo.params.align.alignSJDBoverhangMin}
540 --alignSplicedMateMapLmin ${algo.params.align.alignSplicedMateMapLmin}
541 --alignSplicedMateMapLminOverLmate ${algo.params.align.alignSplicedMateMapLminOverLmate}
542 --alignWindowsPerReadNmax ${algo.params.align.alignWindowsPerReadNmax}
543 --alignTranscriptsPerWindowNmax ${algo.params.align.alignTranscriptsPerWindowNmax}
544 --alignTranscriptsPerReadNmax ${algo.params.align.alignTranscriptsPerReadNmax}
545 --alignEndsType ${algo.params.align.alignEndsType}
546 --peOverlapNbasesMin ${algo.params.align.peOverlapNbasesMin}
547 --peOverlapMMp ${algo.params.align.peOverlapMMp}
548 ## Chimeric alignment parameter options
549 #if str($chimOutType):
550 --chimSegmentMin ${algo.params.chim_settings.chimSegmentMin}
551 --chimScoreMin ${algo.params.chim_settings.chimScoreMin}
552 --chimScoreDropMax $algo.params.chim_settings.chimScoreDropMax
553 --chimScoreSeparation $algo.params.chim_settings.chimScoreSeparation
554 --chimScoreJunctionNonGTAG $algo.params.chim_settings.chimScoreJunctionNonGTAG
555 --chimSegmentReadGapMax $algo.params.chim_settings.chimSegmentReadGapMax
556 --chimFilter $algo.params.chim_settings.chimFilter
557 --chimJunctionOverhangMin $algo.params.chim_settings.chimJunctionOverhangMin
558 --chimMainSegmentMultNmax $algo.params.chim_settings.chimMainSegmentMultNmax
559 #if str($chimOutType) == 'Junctions':
560 --chimMultimapNmax $algo.params.chim_settings.chimMultimapNmax
561 #else:
562 --chimMultimapNmax 0
563 #end if
564 --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange
565 #end if
566
567 ## Limits
568 @LIMITS@
569 ]]></token>
570 <token name="@ALGO_DEFAULT@"><![CDATA[
571 ## Go with STAR's default algorithmic settings,
572 ## but we need to provide a reasonable default
573 ## (taken from STAR-Fusion)
574 ## for --chimSegmentMin in case the user enabled chimeric
575 ## alignments (the STAR default is 0, which disables chimeric
576 ## alignments). For consistency, also set
577 ## --chimMultimapNmax to 1 when chimeric alignments are reported
578 ## in Junctions format only.
579 #if str($chimOutType):
580 --chimSegmentMin 12
581 #if str($chimOutType) == 'Junctions':
582 --chimMultimapNmax 1
583 #end if
584 #end if
585 ]]></token>
586
435 </macros> 587 </macros>