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comparison rg_rnaStar.xml @ 30:4014de1b6daf draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151
author iuc
date Tue, 27 Aug 2024 14:11:16 +0000
parents 3e94726bfa9d
children
comparison
equal deleted inserted replaced
29:b0f2be869d6d 30:4014de1b6daf
45 45
46 --outSAMtype BAM SortedByCoordinate 46 --outSAMtype BAM SortedByCoordinate
47 47
48 ## Two pass mode 48 ## Two pass mode
49 --twopassMode ${twopass.twopassMode} ${twopass.twopass_read_subset} 49 --twopassMode ${twopass.twopassMode} ${twopass.twopass_read_subset}
50 #for $sj_input in $twopass.sj_precalculated: 50 #if str($twopass.sj_precalculated).strip():
51 '$sj_input' 51 #for $sj_input in $twopass.sj_precalculated:
52 #end for 52 '$sj_input'
53 #end for
54 #end if
53 #if str($twopass.twopassMode) != 'None': 55 #if str($twopass.twopassMode) != 'None':
54 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf': 56 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
55 ## need to check first if its a cached index or from history 57 ## need to check first if its a cached index or from history
56 ## if it's cached then the sjdbGTFfile and sjdbOverhang params are not provided 58 ## if it's cached then the sjdbGTFfile and sjdbOverhang params are not provided
57 #if str($refGenomeSource.geneSource) == 'history': 59 #if str($refGenomeSource.geneSource) == 'history':
213 #end if 215 #end if
214 --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange 216 --chimMultimapScoreRange $algo.params.chim_settings.chimMultimapScoreRange
215 #end if 217 #end if
216 218
217 ## Limits 219 ## Limits
218 @LIMITS@ 220 @LIMITS@
219 #else: 221 #else:
220 ## Go with STAR's default algorithmic settings, 222 ## Go with STAR's default algorithmic settings,
221 ## but we need to provide a reasonable default 223 ## but we need to provide a reasonable default
222 ## (taken from STAR-Fusion) 224 ## (taken from STAR-Fusion)
223 ## for --chimSegmentMin in case the user enabled chimeric 225 ## for --chimSegmentMin in case the user enabled chimeric
230 #if str($chimOutType) == 'Junctions': 232 #if str($chimOutType) == 'Junctions':
231 --chimMultimapNmax 1 233 --chimMultimapNmax 1
232 #end if 234 #end if
233 #end if 235 #end if
234 #end if 236 #end if
235
236 --outBAMsortingThreadN \${GALAXY_SLOTS:-4} 237 --outBAMsortingThreadN \${GALAXY_SLOTS:-4}
237 --outBAMsortingBinsN $perf.outBAMsortingBinsN 238 --outBAMsortingBinsN $perf.outBAMsortingBinsN
238 --winAnchorMultimapNmax $perf.winAnchorMultimapNmax 239 --winAnchorMultimapNmax $perf.winAnchorMultimapNmax
239 --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000)) 240 --limitBAMsortRAM \$((\${GALAXY_MEMORY_MB:-0}*1000000))
241
242 #if $oformat.wasp_conditional.waspOutputMode == "wasp_mode":
243 --waspOutputMode SAMtag
244 --varVCFfile '$oformat.wasp_conditional.varVCFfile'
245 #end if
240 246
241 ## Handle chimeric options and output 247 ## Handle chimeric options and output
242 #if str($chimOutType): 248 #if str($chimOutType):
243 --chimOutType $chimOutType 249 --chimOutType $chimOutType
244 #if 'Junctions' in str($chimOutType): 250 #if 'Junctions' in str($chimOutType):
406 truevalue="AllBestScore" falsevalue="OneBestScore" checked="false" 412 truevalue="AllBestScore" falsevalue="OneBestScore" checked="false"
407 label="Would you like all alignments with the best score labeled 413 label="Would you like all alignments with the best score labeled
408 primary?"/> --> 414 primary?"/> -->
409 <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" /> 415 <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />
410 <expand macro="outSAMmapqUnique"/> 416 <expand macro="outSAMmapqUnique"/>
417 <expand macro="wasp"/>
411 </section> 418 </section>
412 <section name="filter" title="Output filter criteria" expanded="true"> 419 <section name="filter" title="Output filter criteria" expanded="true">
413 <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true" 420 <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true"
414 label="Exclude the following records from the BAM output"> 421 label="Exclude the following records from the BAM output">
415 <option value="exclude_unmapped">Unmapped reads</option> 422 <option value="exclude_unmapped">Unmapped reads</option>
563 <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter> 570 <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter>
564 <expand macro="outCountActions" /> 571 <expand macro="outCountActions" />
565 </data> 572 </data>
566 <expand macro="outWigOutputs"/> 573 <expand macro="outWigOutputs"/>
567 </outputs> 574 </outputs>
568
569 <tests> 575 <tests>
570 <test expect_num_outputs="3"> 576 <test expect_num_outputs="3">
571 <conditional name="singlePaired"> 577 <conditional name="singlePaired">
572 <param name="sPaired" value="single" /> 578 <param name="sPaired" value="paired" />
573 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> 579 <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />
574 </conditional> 580 <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />
575 <conditional name="refGenomeSource"> 581 </conditional>
576 <param name="geneSource" value="history" /> 582 <conditional name="refGenomeSource">
577 <param name="genomeFastaFiles" value="tophat_test.fa.gz" /> 583 <param name="geneSource" value="history" />
584 <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />
578 <param name="genomeSAindexNbases" value="5" /> 585 <param name="genomeSAindexNbases" value="5" />
579 </conditional> 586 </conditional>
580 <section name="oformat"> 587 <section name="oformat">
581 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" /> 588 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
589 <conditional name="wasp_conditional">
590 <param name="waspOutputMode" value="wasp_mode"/>
591 <param name="varVCFfile" value="filtered3.vcf" ftype="vcf" />
592 </conditional>
582 </section> 593 </section>
583 <section name="algo"> 594 <section name="algo">
584 <conditional name="params"> 595 <conditional name="params">
585 <param name="settingsType" value="default" /> 596 <param name="settingsType" value="default" />
586 </conditional> 597 </conditional>
587 </section> 598 </section>
588 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> 599 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
589 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> 600 <output name="splice_junctions" file="rnastar_test_splicejunctions_wasp.bed"/>
590 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
591 </test> 601 </test>
592 <!-- test with cached genome index --> 602 <!-- test with cached genome index -->
593 <test expect_num_outputs="3"> 603 <test expect_num_outputs="3">
594 <conditional name="singlePaired"> 604 <conditional name="singlePaired">
595 <param name="sPaired" value="single" /> 605 <param name="sPaired" value="single" />