Mercurial > repos > iuc > rgrnastar

comparison rg_rnaStar.xml @ 27:79de45b5069b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 65fa34f035934b4e9c1fbeb5dffe00b12e6a0f32
author iuc
date Fri, 01 Sep 2023 13:17:29 +0000
parents 4df95e2d7f61
children 3e94726bfa9d
comparison
equal deleted inserted replaced
26:3ea5a2a63fa2 27:79de45b5069b
626 <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" />
627 <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" /> 628 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
629 </output> 629 </output>
630 </test> 630 </test>
631 <!-- Test if an alternative feature can be provided as a splicing unit.
632 If the splice feature set is not set correctly,
633 "Fatal INPUT FILE error, no exon lines in the GTF file" is expected -->
634 <test expect_num_outputs="4">
635 <conditional name="singlePaired">
636 <param name="sPaired" value="single" />
637 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
638 </conditional>
639 <conditional name="refGenomeSource">
640 <param name="geneSource" value="history" />
641 <param name="genomeFastaFiles" value="tophat_test.fa" />
642 <param name="genomeSAindexNbases" value="5" />
643 <conditional name="GTFconditional">
644 <param name="GTFselect" value="with-gtf" />
645 <param name="sjdbOverhang" value="75"/>
646 <param name="sjdbGTFfile" value="no_exon.gtf" ftype="gtf"/>
647 <param name="sjdbGTFfeatureExon" value="fakexon"/>
648 <conditional name="quantmode_output">
649 <param name="quantMode" value="GeneCounts"/>
650 </conditional>
651 </conditional>
652 </conditional>
653 <section name="oformat">
654 <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />
655 </section>
656 <section name="algo">
657 <conditional name="params">
658 <param name="settingsType" value="default" />
659 </conditional>
660 </section>
661
662 <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />
663 <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>
664 <output name="mapped_reads" file="rnastar_test_mapped_reads_fakexon.bam" compare="sim_size" delta="634" />
665 <output name="reads_per_gene" file="tophat_test_reads_per_gene.txt">
666 <metadata name="column_names" value="GeneID,Counts_unstrand,Counts_firstStrand,Counts_secondStrand" />
667 </output>
668 </test>
631 <!-- test gtf file and TranscriptomeSAM mode --> 669 <!-- test gtf file and TranscriptomeSAM mode -->
632 <test expect_num_outputs="4"> 670 <test expect_num_outputs="4">
633 <conditional name="singlePaired"> 671 <conditional name="singlePaired">
634 <param name="sPaired" value="single" /> 672 <param name="sPaired" value="single" />
635 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" /> 673 <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />