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comparison rg_rnaStar.xml @ 23:a2b0feda6933 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
author iuc
date Fri, 17 Feb 2023 20:03:27 +0000
parents 980d2a2e1180
children 4df95e2d7f61
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22:980d2a2e1180 23:a2b0feda6933
1 <tool id="rna_star" name="RNA STAR" version="@VERSION@+galaxy1" profile="20.01" license="MIT"> 1 <tool id="rna_star" name="RNA STAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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="edam"/> 6 <expand macro="edam"/>
63 #end if 63 #end if
64 #end if 64 #end if
65 #end if 65 #end if
66 #end if 66 #end if
67 67
68 --quantMode ${quantmode_output.quantMode} 68 --quantMode ${refGenomeSource.GTFconditional.quantmode_output.quantMode}
69 #if 'TranscriptomeSAM' in str($quantmode_output.quantMode): 69 #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
70 --quantTranscriptomeBan ${quantmode_output.quantTranscriptomeBan} 70 --quantTranscriptomeBan ${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeBan}
71 #end if 71 #end if
72 72
73 ## Output format parameters 73 ## Output format parameters
74 74
75 ## Read tags 75 ## Read tags
204 #end if 204 #end if
205 --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange 205 --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange
206 #end if 206 #end if
207 207
208 ## Limits 208 ## Limits
209 --limitOutSJoneRead $algo.params.limits.limitOutSJoneRead 209 @LIMITS@
210 --limitOutSJcollapsed $algo.params.limits.limitOutSJcollapsed
211 --limitSjdbInsertNsj $algo.params.limits.limitSjdbInsertNsj
212 #else: 210 #else:
213 ## Go with STAR's default algorithmic settings, 211 ## Go with STAR's default algorithmic settings,
214 ## but we need to provide a reasonable default 212 ## but we need to provide a reasonable default
215 ## (taken from STAR-Fusion) 213 ## (taken from STAR-Fusion)
216 ## for --chimSegmentMin in case the user enabled chimeric 214 ## for --chimSegmentMin in case the user enabled chimeric
236 --chimOutType $chimOutType 234 --chimOutType $chimOutType
237 #if 'Junctions' in str($chimOutType): 235 #if 'Junctions' in str($chimOutType):
238 --chimOutJunctionFormat 1 236 --chimOutJunctionFormat 1
239 #end if 237 #end if
240 #end if 238 #end if
239
240 ##outWig:
241 @OUTWIG@
241 && 242 &&
242 ## recompress BAM output for smaller file size 243 ## recompress BAM output for smaller file size
243 samtools view -b -o '$mapped_reads' Aligned.sortedByCoord.out.bam 244 samtools view -b -o '$mapped_reads' Aligned.sortedByCoord.out.bam
244 #if 'TranscriptomeSAM' in str($quantmode_output.quantMode): 245 #if 'TranscriptomeSAM' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):
245 ## same recompression for optional transcriptome BM 246 ## same recompression for optional transcriptome BM
246 && 247 &&
247 samtools view -b -o '$transcriptome_mapped_reads' Aligned.toTranscriptome.out.bam 248 samtools view -b -o '$transcriptome_mapped_reads' Aligned.toTranscriptome.out.bam
248 #end if 249 #end if
250 ##outWig:
251 @OUTWIGOUTPUTS@
249 ]]></command> 252 ]]></command>
250 253
251 <inputs> 254 <inputs>
252 <!-- FASTQ input(s) and options specifically for paired-end data. --> 255 <!-- FASTQ input(s) and options specifically for paired-end data. -->
253 <conditional name="singlePaired"> 256 <conditional name="singlePaired">
277 <when value="indexed"> 280 <when value="indexed">
278 <conditional name="GTFconditional"> 281 <conditional name="GTFconditional">
279 <param name="GTFselect" type="select" 282 <param name="GTFselect" type="select"
280 label="Reference genome with or without an annotation" 283 label="Reference genome with or without an annotation"
281 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and, optionally, provide your own splice-junction annonations."> 284 help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions, and, optionally, provide your own splice-junction annonations.">
282 <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option> 285 <option value="without-gtf-with-gtf" selected='true'>use genome reference without builtin gene-model but provide a gtf</option>
286 <option value="without-gtf">use genome reference without builtin gene-model and do not provide a gtf</option>
283 <option value="with-gtf">use genome reference with builtin gene-model</option> 287 <option value="with-gtf">use genome reference with builtin gene-model</option>
284 </param> 288 </param>
285 <when value="with-gtf"> 289 <when value="with-gtf">
286 <expand macro="index_selection" with_gene_model="1" /> 290 <expand macro="index_selection" with_gene_model="1" />
291 <expand macro="quantMode" />
292 </when>
293 <when value="without-gtf-with-gtf">
294 <expand macro="index_selection" with_gene_model="0" />
295 <expand macro="SJDBOPTIONS"/>
296 <expand macro="quantMode" />
287 </when> 297 </when>
288 <when value="without-gtf"> 298 <when value="without-gtf">
289 <expand macro="index_selection" with_gene_model="0" /> 299 <expand macro="index_selection" with_gene_model="0" />
290 <expand macro="@SJDBOPTIONS@" /> 300 <expand macro="quantModeNoGTF" />
291 </when> 301 </when>
292 </conditional> 302 </conditional>
293 </when> 303 </when>
294 <when value="history"> 304 <when value="history">
295 <expand macro="ref_selection" /> 305 <expand macro="ref_selection" />
299 help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome."> 309 help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome.">
300 <option value="without-gtf">build index without gene-model</option> 310 <option value="without-gtf">build index without gene-model</option>
301 <option value="with-gtf">build index with gene-model</option> 311 <option value="with-gtf">build index with gene-model</option>
302 </param> 312 </param>
303 <when value="with-gtf"> 313 <when value="with-gtf">
304 <expand macro="@SJDBOPTIONS@" optional="false"/> 314 <expand macro="SJDBOPTIONS"/>
315 <expand macro="quantMode" />
305 </when> 316 </when>
306 <when value="without-gtf" /> 317 <when value="without-gtf">
318 <expand macro="quantModeNoGTF" />
319 </when>
307 </conditional> 320 </conditional>
308 </when> 321 </when>
309 </conditional> 322 </conditional>
310 323
311 <conditional name="twopass"> 324 <conditional name="twopass">
333 <param name="twopass_read_subset" type="hidden" value="" /> 346 <param name="twopass_read_subset" type="hidden" value="" />
334 <param name="sj_precalculated" type="data" multiple="true" format="interval" 347 <param name="sj_precalculated" type="data" multiple="true" format="interval"
335 label="Pregenerated splice junctions datasets of your samples" /> 348 label="Pregenerated splice junctions datasets of your samples" />
336 </when> 349 </when>
337 </conditional> 350 </conditional>
338 <conditional name="quantmode_output">
339 <param argument="--quantMode" type="select"
340 label="Per gene/transcript output"
341 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!">
342 <option value="-">No per gene or transcript output</option>
343 <option value="GeneCounts">Per gene read counts (GeneCounts)</option>
344 <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>
345 <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>
346 </param>
347 <when value="-" />
348 <when value="GeneCounts" />
349 <when value="TranscriptomeSAM">
350 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
351 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
352 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." />
353 </when>
354 <when value="TranscriptomeSAM GeneCounts">
355 <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"
356 label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"
357 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." />
358 </when>
359 </conditional>
360 <param argument="--chimOutType" type="select" 351 <param argument="--chimOutType" type="select"
361 label="Report chimeric alignments?" 352 label="Report chimeric alignments?"
362 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."> 353 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.">
363 <option value="">Don't report chimeric alignments</option> 354 <option value="">Don't report chimeric alignments</option>
364 <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option> 355 <option value="Junctions">As separate tabular "Junctions" output (Junctions)</option>
365 <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option> 356 <option value="WithinBAM">Within the BAM output (together with regular alignments; WithinBAM)</option>
366 <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option> 357 <option value="WithinBAM HardClip">Within the BAM output (together with regular alignments; WithinBAM HardClip) hard-clipping in the CIGAR for supplemental chimeric alignments</option>
367 <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option> 358 <option value="WithinBAM SoftClip">Within the BAM output (together with regular alignments; WithinBAM SoftClip) soft-clipping in the CIGAR for supplemental chimeric alignments</option>
368 <option value="WithinBAM Junctions">Deprecated: In both forms (WithinBAM Junctions)</option>
369 </param> 359 </param>
370 360
371 <section name="oformat" title="BAM output format specification" expanded="true"> 361 <section name="oformat" title="BAM output format specification" expanded="true">
372 <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true" 362 <param argument="--outSAMattributes" type="select" display="checkboxes" multiple="true" optional="true"
373 label="Read alignment tags to include in the BAM output" 363 label="Read alignment tags to include in the BAM output"
374 help="Note on using the XS tag: If the XS tag is used, STAR will filter out alignments with undefined strand (i.e., those containing only non-canonical unannotated junctions). Using this tag is recommended if you plan to use the STAR results with STAR-Fusion. In addition, it is required for compatibility 364 help="Note on using the XS tag: If the XS tag is used, STAR will filter out alignments with undefined strand (i.e., those containing only non-canonical unannotated junctions). Using this tag is recommended if you plan to use the STAR results with STAR-Fusion. In addition, it is required for compatibility
375 with Cufflinks if your sequences come from an unstranded library preparation."> 365 with Cufflinks if your sequences come from an unstranded library preparation.">
376 <option value="NH" selected="true">NH (number of reported alignments/hits for the read)</option> 366 <expand macro="common_SAM_attributes"/>
377 <option value="HI" selected="true">HI (query hit index)</option> 367 <option value="MC">MC (CIGAR string for mate/next segment)</option>
378 <option value="AS" selected="true">AS (local alignment score)</option>
379 <option value="nM" selected="true">nM (number of mismatches per (paired) alignment)</option>
380 <option value="XS">XS (strand flag, see parameter help below) </option> 368 <option value="XS">XS (strand flag, see parameter help below) </option>
381 <option value="NM">NM (edit distance of the aligned read to the reference)</option> 369 <option value="ch" selected="true">ch (used to indicate chimeric alignments)</option> <!--This is not the default in STAR-->
382 <option value="MD">MD (string for mismatching positions)</option>
383 <option value="MC">MC (CIGAR string for mate/next segment)</option>
384 <option value="jM">jM (intron motifs for all junctions)</option>
385 <option value="jI">jI (1-based start and end of introns for all junctions)</option>
386 <option value="ch" selected="true">ch (used to indicate chimeric alignments)</option>
387 </param> 370 </param>
388 <param argument="--outSAMattrIHstart" name="HI_offset" type="select" display="radio" 371 <param argument="--outSAMattrIHstart" name="HI_offset" type="select" display="radio"
389 label="HI tag values should be"> 372 label="HI tag values should be">
390 <option value="1" selected="true">one-based</option> 373 <option value="1" selected="true">one-based</option>
391 <option value="0">zero-based</option> 374 <option value="0">zero-based</option>
401 <param argument="- -outSAMprimaryFlag" type="boolean" 384 <param argument="- -outSAMprimaryFlag" type="boolean"
402 truevalue="AllBestScore" falsevalue="OneBestScore" checked="false" 385 truevalue="AllBestScore" falsevalue="OneBestScore" checked="false"
403 label="Would you like all alignments with the best score labeled 386 label="Would you like all alignments with the best score labeled
404 primary?"/> --> 387 primary?"/> -->
405 <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" /> 388 <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />
406 <param argument="--outSAMmapqUnique" type="integer" value="60" min="30" max="255" 389 <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value
390 - according to SAM/BAM specs it means "undefined".
391 - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->
392 <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"
407 label="MAPQ value for unique mappers" 393 label="MAPQ value for unique mappers"
408 help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is 394 help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is
409 used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflinks." /> 395 used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />
410 </section> 396 </section>
411 <section name="filter" title="Output filter criteria" expanded="true"> 397 <section name="filter" title="Output filter criteria" expanded="true">
412 <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true" 398 <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true"
413 label="Exclude the following records from the BAM output"> 399 label="Exclude the following records from the BAM output">
414 <option value="exclude_unmapped">Unmapped reads</option> 400 <option value="exclude_unmapped">Unmapped reads</option>
467 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/> 453 <param argument="--seedPerWindowNmax" type="integer" min="1" value="50" label="Maximum number of seeds per window"/>
468 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/> 454 <param argument="--seedNoneLociPerWindow" type="integer" min="1" value="10" label="Maximum number of one seed loci per window"/>
469 </section> 455 </section>
470 456
471 <section name="align" title="Alignment parameters" expanded="false"> 457 <section name="align" title="Alignment parameters" expanded="false">
472 <param argument="--alignIntronMin" name="alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/> 458 <param argument="--alignIntronMin" type="integer" min="0" value="21" label="Minimum intron size"/>
473 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/> 459 <param argument="--alignIntronMax" type="integer" min="0" value="0" label="Maximum intron size"/>
474 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/> 460 <param argument="--alignMatesGapMax" type="integer" min="0" value="0" label="Maximum gap between two mates"/>
475 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/> 461 <param argument="--alignSJoverhangMin" type="integer" min="1" value="5" label="Minimum overhang for spliced alignments"/>
476 <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true"> 462 <section name="alignSJstitchMismatchNmax" title="Maximum number of mismatches for stitching of the splice junctions (-1: no limit)" expanded="true">
477 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/> 463 <param argument="--alignSJstitchMismatchNmax" name="alignSJstitchMismatchNmax1" type="integer" min="-1" value="0" label="Non-canonical motifs"/>
483 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/> 469 <param argument="--alignSplicedMateMapLmin" type="integer" min="0" value="0" label="Minimum mapped length for a read mate that is spliced"/>
484 <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"/> 470 <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"/>
485 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/> 471 <param argument="--alignWindowsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of windows per read"/>
486 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/> 472 <param argument="--alignTranscriptsPerWindowNmax" type="integer" min="1" value="100" label="Maximum number of transcripts per window"/>
487 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/> 473 <param argument="--alignTranscriptsPerReadNmax" type="integer" min="1" value="10000" label="Maximum number of different alignments per read to consider"/>
488 <param argument="--alignEndsType" type="boolean" truevalue="EndToEnd" falsevalue="Local" checked="false" label="Use end-to-end read alignments, with no soft-clipping?"/> 474 <param argument="--alignEndsType" type="select" label="type of read ends alignment">
475 <option value="Local">standard local alignment with soft-clipping allowed</option>
476 <option value="EndToEnd">force end-to-end read alignment, do not soft-clip</option>
477 <option value="Extend5pOfRead1">fully extend only the 5p of the read1, all other ends: local alignment</option>
478 <option value="Extend5pOfReads12">fully extend only the 5p of the both read1 and read2, all other ends: local alignment</option>
479 </param>
489 <param argument="--peOverlapNbasesMin" type="integer" min="0" value="0" 480 <param argument="--peOverlapNbasesMin" type="integer" min="0" value="0"
490 label="minimum number of overlap bases to trigger mates merging and realignment" /> 481 label="minimum number of overlap bases to trigger mates merging and realignment" />
491 <param argument="--peOverlapMMp" type="float" min="0" max="1" value="0.01" 482 <param argument="--peOverlapMMp" type="float" min="0" max="1" value="0.01"
492 label="maximum proportion of mismatched bases in the overlap area" /> 483 label="maximum proportion of mismatched bases in the overlap area" />
493 </section> 484 </section>
517 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. " /> 508 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. " />
518 <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1" 509 <param argument="--chimMultimapScoreRange" type="integer" min="0" value="1"
519 label="Score range for multi-mapping chimeras" 510 label="Score range for multi-mapping chimeras"
520 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" /> 511 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" />
521 </section> 512 </section>
522 <section name="limits" title="Limits" expanded="false"> 513 <expand macro="limits" />
523 <param argument="--limitOutSJoneRead" type="integer" min="1" value="1000" label="Maximum number of junctions for one read (including all multimappers)" />
524 <param argument="--limitOutSJcollapsed" type="integer" min="1" value="1000000" label="Maximum number of collapsed junctions" />
525 <param argument="--limitSjdbInsertNsj" type="integer" min="0" value="1000000" label="Maximum number of inserts to be inserted into the genome on the fly." />
526 </section>
527 </when> 514 </when>
528 </conditional> 515 </conditional>
529 </section> 516 </section>
530 <section name="perf" title="Performance tweaks / Troubleshooting" expanded="false"> 517 <section name="perf" title="Performance tweaks / Troubleshooting" expanded="false">
531 <param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50. Tweak this if you are facing memory-related errors." /> 518 <param argument="--outBAMsortingBinsN" type="integer" value="50" min="1" label="Number of genome bins for coordinate-sorting" help="Higher values result in lower RAM requirements during the sorting step. The default value is 50. Tweak this if you are facing memory-related errors." />
532 <param argument="--winAnchorMultimapNmax" type="integer" value="50" min="50" label="Maximum number of loci anchors are allowed to map to" help="Higher value can increase the runtime singificantly. This value should be set greater or equal to --outFilterMultimapNmax" /> 519 <param argument="--winAnchorMultimapNmax" type="integer" value="50" min="50" label="Maximum number of loci anchors are allowed to map to" help="Higher value can increase the runtime singificantly. This value should be set greater or equal to --outFilterMultimapNmax" />
533 </section> 520 </section>
521 <expand macro="outWig"/>
534 </inputs> 522 </inputs>
535 523
536 <outputs> 524 <outputs>
537 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"> 525 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out">
538 <expand macro="dbKeyActions" /> 526 <expand macro="dbKeyActions" />
550 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam"> 538 <data name="mapped_reads" format="bam" label="${tool.name} on ${on_string}: mapped.bam">
551 <expand macro="dbKeyActions" /> 539 <expand macro="dbKeyActions" />
552 </data> 540 </data>
553 541
554 <data name="transcriptome_mapped_reads" format="unsorted.bam" label="${tool.name} on ${on_string}: transcriptome-mapped.bam" > 542 <data name="transcriptome_mapped_reads" format="unsorted.bam" label="${tool.name} on ${on_string}: transcriptome-mapped.bam" >
555 <filter>'TranscriptomeSAM' in quantmode_output['quantMode']</filter> 543 <filter>'TranscriptomeSAM' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter>
556 <expand macro="dbKeyActions" /> 544 <expand macro="dbKeyActions" />
557 </data> 545 </data>
558 546
559 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab"> 547 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
560 <filter>'GeneCounts' in quantmode_output['quantMode']</filter> 548 <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter>
561 <expand macro="dbKeyActions" /> 549 <expand macro="dbKeyActions" />
550 <expand macro="outCountActions" />
562 </data> 551 </data>
552 <expand macro="outWigOutputs"/>
563 </outputs> 553 </outputs>
564 554
565 <tests> 555 <tests>
566 <test expect_num_outputs="3"> 556 <test expect_num_outputs="3">
567 <conditional name="singlePaired"> 557 <conditional name="singlePaired">
568 <param name="sPaired" value="single" /> 558 <param name="sPaired" value="single" />
569 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> 559 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
570 </conditional> 560 </conditional>
571 <conditional name="refGenomeSource"> 561 <conditional name="refGenomeSource">
572 <param name="geneSource" value="history" /> 562 <param name="geneSource" value="history" />
573 <param name="genomeFastaFiles" value="tophat_test.fa" /> 563 <param name="genomeFastaFiles" value="tophat_test.fa.gz" />
574 <param name="genomeSAindexNbases" value="5" /> 564 <param name="genomeSAindexNbases" value="5" />
575 </conditional> 565 </conditional>
576 <section name="oformat"> 566 <section name="oformat">
577 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 567 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
578 <param name="outSAMmapqUnique" value="255" />
579 </section> 568 </section>
580 <section name="algo"> 569 <section name="algo">
581 <conditional name="params"> 570 <conditional name="params">
582 <param name="settingsType" value="default" /> 571 <param name="settingsType" value="default" />
583 </conditional> 572 </conditional>
599 <param name="genomeDir" value="001" /> 588 <param name="genomeDir" value="001" />
600 </conditional> 589 </conditional>
601 </conditional> 590 </conditional>
602 <section name="oformat"> 591 <section name="oformat">
603 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 592 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
604 <param name="outSAMmapqUnique" value="255" />
605 </section> 593 </section>
606 <section name="algo"> 594 <section name="algo">
607 <conditional name="params"> 595 <conditional name="params">
608 <param name="settingsType" value="default" /> 596 <param name="settingsType" value="default" />
609 </conditional> 597 </conditional>
624 <param name="genomeSAindexNbases" value="5" /> 612 <param name="genomeSAindexNbases" value="5" />
625 <conditional name="GTFconditional"> 613 <conditional name="GTFconditional">
626 <param name="GTFselect" value="with-gtf" /> 614 <param name="GTFselect" value="with-gtf" />
627 <param name="sjdbOverhang" value="75"/> 615 <param name="sjdbOverhang" value="75"/>
628 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> 616 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
629 </conditional> 617 <conditional name="quantmode_output">
630 </conditional> 618 <param name="quantMode" value="GeneCounts"/>
631 <conditional name="quantmode_output"> 619 </conditional>
632 <param name="quantMode" value="GeneCounts"/> 620 </conditional>
633 </conditional> 621 </conditional>
634 <section name="oformat"> 622 <section name="oformat">
635 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 623 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
636 <param name="outSAMmapqUnique" value="255" />
637 </section> 624 </section>
638 <section name="algo"> 625 <section name="algo">
639 <conditional name="params"> 626 <conditional name="params">
640 <param name="settingsType" value="default" /> 627 <param name="settingsType" value="default" />
641 </conditional> 628 </conditional>
658 <param name="genomeSAindexNbases" value="5" /> 645 <param name="genomeSAindexNbases" value="5" />
659 <conditional name="GTFconditional"> 646 <conditional name="GTFconditional">
660 <param name="GTFselect" value="with-gtf" /> 647 <param name="GTFselect" value="with-gtf" />
661 <param name="sjdbOverhang" value="75"/> 648 <param name="sjdbOverhang" value="75"/>
662 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/> 649 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
663 </conditional> 650 <conditional name="quantmode_output">
664 </conditional> 651 <param name="quantMode" value="TranscriptomeSAM"/>
665 <conditional name="quantmode_output"> 652 </conditional>
666 <param name="quantMode" value="TranscriptomeSAM"/> 653 </conditional>
667 </conditional> 654 </conditional>
668 <section name="oformat"> 655 <section name="oformat">
669 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 656 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
670 <param name="outSAMmapqUnique" value="255" />
671 </section> 657 </section>
672 <section name="algo"> 658 <section name="algo">
673 <conditional name="params"> 659 <conditional name="params">
674 <param name="settingsType" value="default" /> 660 <param name="settingsType" value="default" />
675 </conditional> 661 </conditional>
678 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> 664 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
679 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> 665 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
680 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> 666 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
681 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" /> 667 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" />
682 </test> 668 </test>
669 <!-- test cached no index but gtf file and GeneCounts TranscriptomeSAM mode -->
670 <test expect_num_outputs="5">
671 <conditional name="singlePaired">
672 <param name="sPaired" value="single" />
673 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
674 </conditional>
675 <conditional name="refGenomeSource">
676 <param name="geneSource" value="indexed" />
677 <conditional name="GTFconditional">
678 <param name="GTFselect" value="without-gtf-with-gtf" />
679 <param name="genomeDir" value="000" />
680 <param name="sjdbOverhang" value="75"/>
681 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
682 <conditional name="quantmode_output">
683 <param name="quantMode" value="TranscriptomeSAM GeneCounts"/>
684 </conditional>
685 </conditional>
686 </conditional>
687 <section name="oformat">
688 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
689 </section>
690 <section name="algo">
691 <conditional name="params">
692 <param name="settingsType" value="default" />
693 </conditional>
694 </section>
695
696 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
697 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
698 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
699 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" />
700 <output name="transcriptome_mapped_reads" file="rnastar_test_transcriptome_mapped_reads.bam" compare="sim_size" delta="634" />
701 </test>
683 <test expect_num_outputs="3"> 702 <test expect_num_outputs="3">
684 <conditional name="singlePaired"> 703 <conditional name="singlePaired">
685 <param name="sPaired" value="single" /> 704 <param name="sPaired" value="single" />
686 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> 705 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
687 </conditional> 706 </conditional>
690 <param name="genomeFastaFiles" value="tophat_test.fa" /> 709 <param name="genomeFastaFiles" value="tophat_test.fa" />
691 <param name="genomeSAindexNbases" value="5" /> 710 <param name="genomeSAindexNbases" value="5" />
692 </conditional> 711 </conditional>
693 <section name="oformat"> 712 <section name="oformat">
694 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" /> 713 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" />
695 <param name="outSAMmapqUnique" value="255" />
696 </section> 714 </section>
697 <section name="filter"> 715 <section name="filter">
698 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> 716 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
699 <conditional name="output_params2"> 717 <conditional name="output_params2">
700 <param name="output_select2" value="yes" /> 718 <param name="output_select2" value="yes" />
726 <param name="genomeSAindexNbases" value="5" /> 744 <param name="genomeSAindexNbases" value="5" />
727 </conditional> 745 </conditional>
728 <param name="chimOutType" value="Junctions" /> 746 <param name="chimOutType" value="Junctions" />
729 <section name="oformat"> 747 <section name="oformat">
730 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" /> 748 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" />
731 <param name="outSAMmapqUnique" value="255" />
732 </section> 749 </section>
733 <section name="algo"> 750 <section name="algo">
734 <conditional name="params"> 751 <conditional name="params">
735 <param name="settingsType" value="star_fusion" /> 752 <param name="settingsType" value="star_fusion" />
736 </conditional> 753 </conditional>
749 <param name="genomeSAindexNbases" value="5" /> 766 <param name="genomeSAindexNbases" value="5" />
750 </conditional> 767 </conditional>
751 <param name="chimOutType" value="Junctions" /> 768 <param name="chimOutType" value="Junctions" />
752 <section name="oformat"> 769 <section name="oformat">
753 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" /> 770 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch,XS" />
754 <param name="outSAMmapqUnique" value="255" />
755 </section> 771 </section>
756 <section name="algo"> 772 <section name="algo">
757 <conditional name="params"> 773 <conditional name="params">
758 <param name="settingsType" value="star_fusion" /> 774 <param name="settingsType" value="star_fusion" />
759 </conditional> 775 </conditional>
771 <param name="genomeFastaFiles" value="tophat_test.fa" /> 787 <param name="genomeFastaFiles" value="tophat_test.fa" />
772 <param name="genomeSAindexNbases" value="5" /> 788 <param name="genomeSAindexNbases" value="5" />
773 </conditional> 789 </conditional>
774 <section name="oformat"> 790 <section name="oformat">
775 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 791 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
776 <param name="outSAMmapqUnique" value="255" />
777 </section> 792 </section>
778 <section name="filter"> 793 <section name="filter">
779 <param name="basic_filters" value="--outFilterIntronMotifs RemoveNoncanonical" /> 794 <param name="basic_filters" value="--outFilterIntronMotifs RemoveNoncanonical" />
780 <conditional name="output_params2"> 795 <conditional name="output_params2">
781 <param name="output_select2" value="yes" /> 796 <param name="output_select2" value="yes" />
806 <conditional name="twopass"> 821 <conditional name="twopass">
807 <param name="twopassMode" value="Basic" /> 822 <param name="twopassMode" value="Basic" />
808 </conditional> 823 </conditional>
809 <section name="oformat"> 824 <section name="oformat">
810 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 825 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
811 <param name="outSAMmapqUnique" value="255" />
812 </section> 826 </section>
813 <section name="filter"> 827 <section name="filter">
814 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> 828 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
815 <conditional name="output_params2"> 829 <conditional name="output_params2">
816 <param name="output_select2" value="yes" /> 830 <param name="output_select2" value="yes" />
842 <conditional name="twopass"> 856 <conditional name="twopass">
843 <param name="twopassMode" value="Basic" /> 857 <param name="twopassMode" value="Basic" />
844 </conditional> 858 </conditional>
845 <section name="oformat"> 859 <section name="oformat">
846 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 860 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
847 <param name="outSAMmapqUnique" value="255" />
848 </section> 861 </section>
849 <section name="filter"> 862 <section name="filter">
850 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> 863 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
851 <conditional name="output_params2"> 864 <conditional name="output_params2">
852 <param name="output_select2" value="yes" /> 865 <param name="output_select2" value="yes" />
878 <conditional name="twopass"> 891 <conditional name="twopass">
879 <param name="twopassMode" value="Basic" /> 892 <param name="twopassMode" value="Basic" />
880 </conditional> 893 </conditional>
881 <section name="oformat"> 894 <section name="oformat">
882 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 895 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
883 <param name="outSAMmapqUnique" value="255" />
884 </section> 896 </section>
885 <section name="filter"> 897 <section name="filter">
886 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" /> 898 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonical" />
887 <conditional name="output_params2"> 899 <conditional name="output_params2">
888 <param name="output_select2" value="yes" /> 900 <param name="output_select2" value="yes" />
913 <param name="twopassMode" value="None --sjdbFileChrStartEnd" /> 925 <param name="twopassMode" value="None --sjdbFileChrStartEnd" />
914 <param name="sj_precalculated" value="rnastar_test_splicejunctions_twopass.bed" /> 926 <param name="sj_precalculated" value="rnastar_test_splicejunctions_twopass.bed" />
915 </conditional> 927 </conditional>
916 <section name="oformat"> 928 <section name="oformat">
917 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 929 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
918 <param name="outSAMmapqUnique" value="255" />
919 </section> 930 </section>
920 <section name="filter"> 931 <section name="filter">
921 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonicalUnannotated,--outFilterIntronMotifs RemoveNoncanonical" /> 932 <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonicalUnannotated,--outFilterIntronMotifs RemoveNoncanonical" />
922 <conditional name="output_params2"> 933 <conditional name="output_params2">
923 <param name="output_select2" value="yes" /> 934 <param name="output_select2" value="yes" />
944 <param name="genomeFastaFiles" value="tophat_test.fa" /> 955 <param name="genomeFastaFiles" value="tophat_test.fa" />
945 <param name="genomeSAindexNbases" value="14" /> 956 <param name="genomeSAindexNbases" value="14" />
946 </conditional> 957 </conditional>
947 <section name="oformat"> 958 <section name="oformat">
948 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 959 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
949 <param name="outSAMmapqUnique" value="255" />
950 </section> 960 </section>
951 <section name="algo"> 961 <section name="algo">
952 <conditional name="params"> 962 <conditional name="params">
953 <param name="settingsType" value="default" /> 963 <param name="settingsType" value="default" />
954 </conditional> 964 </conditional>
967 <param name="genomeFastaFiles" value="tophat_test.fa" /> 977 <param name="genomeFastaFiles" value="tophat_test.fa" />
968 <param name="genomeSAindexNbases" value="10" /> 978 <param name="genomeSAindexNbases" value="10" />
969 </conditional> 979 </conditional>
970 <section name="oformat"> 980 <section name="oformat">
971 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 981 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
972 <param name="outSAMmapqUnique" value="255" />
973 </section> 982 </section>
974 <section name="algo"> 983 <section name="algo">
975 <conditional name="params"> 984 <conditional name="params">
976 <param name="settingsType" value="default" /> 985 <param name="settingsType" value="default" />
977 </conditional> 986 </conditional>
978 </section> 987 </section>
979 <output name="output_log" file="rnastar_test_genomeSAindexNbases_02.log" compare="re_match_multiline" /> 988 <output name="output_log" file="rnastar_test_genomeSAindexNbases_02.log" compare="re_match_multiline" />
980 <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases_02.bed"/> 989 <output name="splice_junctions" file="rnastar_test_genomeSAindexNbases_02.bed"/>
981 <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases_02.bam" compare="sim_size" delta="634" /> 990 <output name="mapped_reads" file="rnastar_test_mapped_reads_genomeSAindexNbases_02.bam" compare="sim_size" delta="634" />
991 </test>
992 <!-- test paired-end input and outWig -->
993 <test expect_num_outputs="6">
994 <conditional name="singlePaired">
995 <param name="sPaired" value="paired" />
996 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
997 <param name="input2" value="tophat_in3.fastqsanger" ftype="fastqsanger" />
998 </conditional>
999 <conditional name="refGenomeSource">
1000 <param name="geneSource" value="history" />
1001 <param name="genomeFastaFiles" value="tophat_test.fa" />
1002 <param name="genomeSAindexNbases" value="5" />
1003 <conditional name="GTFconditional">
1004 <param name="GTFselect" value="with-gtf" />
1005 <param name="sjdbOverhang" value="75"/>
1006 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
1007 <conditional name="quantmode_output">
1008 <param name="quantMode" value="GeneCounts"/>
1009 </conditional>
1010 </conditional>
1011 </conditional>
1012 <section name="oformat">
1013 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
1014 </section>
1015 <section name="algo">
1016 <conditional name="params">
1017 <param name="settingsType" value="default" />
1018 </conditional>
1019 </section>
1020 <conditional name="outWig">
1021 <param name="outWigType" value="wiggle" />
1022 <param name="outWigTypeSecondWord" value="read2"/>
1023 <param name="outWigStrand" value="false" />
1024 </conditional>
1025 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
1026 <output name="splice_junctions" file="rnastar_test_splicejunctions_PE.bed"/>
1027 <output name="mapped_reads" file="rnastar_test_mapped_reads_PE.bam" compare="sim_size" delta="634" />
1028 <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE.txt" />
1029 <output name="signal_unique_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig"/>
1030 <output name="signal_uniquemultiple_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig" />
1031 </test>
1032 <!-- test paired-end input as collection and outWig stranded -->
1033 <test expect_num_outputs="8">
1034 <conditional name="singlePaired">
1035 <param name="sPaired" value="paired_collection" />
1036 <param name="input" >
1037 <collection type="paired">
1038 <element name="forward" value="tophat_revlib_R1.fastqsanger" ftype="fastq"/>
1039 <element name="reverse" value="tophat_revlib_R2.fastqsanger" ftype="fastq"/>
1040 </collection>
1041 </param>
1042 </conditional>
1043 <conditional name="refGenomeSource">
1044 <param name="geneSource" value="history" />
1045 <param name="genomeFastaFiles" value="tophat_test.fa" />
1046 <param name="genomeSAindexNbases" value="5" />
1047 <conditional name="GTFconditional">
1048 <param name="GTFselect" value="with-gtf" />
1049 <param name="sjdbOverhang" value="75"/>
1050 <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>
1051 <conditional name="quantmode_output">
1052 <param name="quantMode" value="GeneCounts"/>
1053 </conditional>
1054 </conditional>
1055 </conditional>
1056 <section name="oformat">
1057 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
1058 </section>
1059 <section name="algo">
1060 <conditional name="params">
1061 <param name="settingsType" value="default" />
1062 </conditional>
1063 </section>
1064 <conditional name="outWig">
1065 <param name="outWigType" value="bedGraph" />
1066 </conditional>
1067
1068 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
1069 <output name="splice_junctions">
1070 <assert_contents>
1071 <has_n_lines n="2"/>
1072 <has_line_matching expression="test_chromosome\s+251\s+350\s+1\s+1\s+0\s+24\s+0\s+33"/>
1073 <has_line_matching expression="test_chromosome\s+401\s+500\s+1\s+1\s+0\s+25\s+0\s+36"/>
1074 </assert_contents>
1075 </output>
1076 <output name="mapped_reads" >
1077 <assert_contents>
1078 <has_size value="4711" delta="800"/>
1079 </assert_contents>
1080 </output>
1081 <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE_rev.txt" />
1082 <output name="signal_unique_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/>
1083 <output name="signal_uniquemultiple_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/>
1084 <output name="signal_unique_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />
1085 <output name="signal_uniquemultiple_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />
982 </test> 1086 </test>
983 </tests> 1087 </tests>
984 <help><![CDATA[ 1088 <help><![CDATA[
985 **What it does** 1089 **What it does**
986 1090
1022 **Report chimeric alignments?**: `As separate tabular "Junctions" output (Junctions)` or **Report chimeric alignments?**: `Within the BAM output (together with regular alignments; WithinBAM)`. 1126 **Report chimeric alignments?**: `As separate tabular "Junctions" output (Junctions)` or **Report chimeric alignments?**: `Within the BAM output (together with regular alignments; WithinBAM)`.
1023 1127
1024 In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity 1128 In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity
1025 1129
1026 - under *Output filter criteria*, 1130 - under *Output filter criteria*,
1027 **Would you like to set additional output filters?**: select `Yes' to set 1131 **Would you like to set additional output filters?**: select `Yes` to set
1028 **Maximum number of alignments to output a read's alignment results, plus 1** to 50 1132 **Maximum number of alignments to output a read's alignment results, plus 1** to 50
1029 1133
1030 - under *Algorithmic settings*, **Configure seed, alignment and limits options**: 1134 - under *Algorithmic settings*, **Configure seed, alignment and limits options**:
1031 `use parameters suggested for Arriba`. 1135 `use parameters suggested for Arriba`.
1032 1136