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comparison rg_rnaStar.xml @ 24:4df95e2d7f61 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 904cd12820a09a8e7ce7d01c64fa22f1ed93ed17
author iuc
date Wed, 22 Feb 2023 18:00:57 +0000
parents a2b0feda6933
children 79de45b5069b
comparison
equal deleted inserted replaced
23:a2b0feda6933 24:4df95e2d7f61
384 <param argument="- -outSAMprimaryFlag" type="boolean" 384 <param argument="- -outSAMprimaryFlag" type="boolean"
385 truevalue="AllBestScore" falsevalue="OneBestScore" checked="false" 385 truevalue="AllBestScore" falsevalue="OneBestScore" checked="false"
386 label="Would you like all alignments with the best score labeled 386 label="Would you like all alignments with the best score labeled
387 primary?"/> --> 387 primary?"/> -->
388 <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" /> 388 <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />
389 <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value 389 <expand macro="outSAMmapqUnique"/>
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"
393 label="MAPQ value for unique mappers"
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
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." />
396 </section> 390 </section>
397 <section name="filter" title="Output filter criteria" expanded="true"> 391 <section name="filter" title="Output filter criteria" expanded="true">
398 <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true" 392 <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true"
399 label="Exclude the following records from the BAM output"> 393 label="Exclude the following records from the BAM output">
400 <option value="exclude_unmapped">Unmapped reads</option> 394 <option value="exclude_unmapped">Unmapped reads</option>
417 <param argument="--outFilterMismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output"/> 411 <param argument="--outFilterMismatchNoverReadLmax" type="float" value="1" min="0" max="1" label="Maximum ratio of mismatches to read length" help="Alignments with a mismatch ratio of at least this value will not be output"/>
418 <param argument="--outFilterScoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output"/> 412 <param argument="--outFilterScoreMin" type="integer" value="0" min="0" label="Minimum alignment score" help="Alignments must have scores higher than this value to be output"/>
419 <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/> 413 <param argument="--outFilterScoreMinOverLread" type="float" value="0.66" min="0" max="1" label="Minimum alignment score, normalized to read length" help="Alignments must have (normalized) scores higher than this value to be output"/>
420 <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/> 414 <param argument="--outFilterMatchNmin" type="integer" value="0" min="0" label="Minimum number of matched bases" help="Alignments must have the number of matched bases higher than this value to be output"/>
421 <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/> 415 <param argument="--outFilterMatchNminOverLread" type="float" value="0.66" min="0" max="1" label="Minimum number of matched bases, normalized to read length" help="Alignments must have the (normalized) number of matched bases higher than this value to be output"/>
422 <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to –-outFilterMultimapNmax) being output" /> 416 <param argument="--outSAMmultNmax" type="integer" value="-1" min="-1" label="Maximum number of multimapping alignments to output for a read" help="A value of -1 (the default) results in all alignments (up to --outFilterMultimapNmax) being output" />
423 <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN"> 417 <param argument="--outSAMtlen" type="select" label="Calculation method for TLEN">
424 <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option> 418 <option value="1" selected="true">leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate</option>
425 <option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option> 419 <option value="2">leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends</option>
426 </param> 420 </param>
427 </when> 421 </when>
544 <expand macro="dbKeyActions" /> 538 <expand macro="dbKeyActions" />
545 </data> 539 </data>
546 540
547 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab"> 541 <data name="reads_per_gene" format="tabular" label="${tool.name} on ${on_string}: reads per gene" from_work_dir="ReadsPerGene.out.tab">
548 <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter> 542 <filter>'GeneCounts' in refGenomeSource['GTFconditional']['quantmode_output']['quantMode']</filter>
549 <expand macro="dbKeyActions" />
550 <expand macro="outCountActions" /> 543 <expand macro="outCountActions" />
551 </data> 544 </data>
552 <expand macro="outWigOutputs"/> 545 <expand macro="outWigOutputs"/>
553 </outputs> 546 </outputs>
554 547
629 </section> 622 </section>
630 623
631 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" /> 624 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
632 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/> 625 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
633 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /> 626 <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" />
634 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt" /> 627 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt">
628 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
629 </output>
635 </test> 630 </test>
636 <!-- test gtf file and TranscriptomeSAM mode --> 631 <!-- test gtf file and TranscriptomeSAM mode -->
637 <test expect_num_outputs="4"> 632 <test expect_num_outputs="4">
638 <conditional name="singlePaired"> 633 <conditional name="singlePaired">
639 <param name="sPaired" value="single" /> 634 <param name="sPaired" value="single" />