name: rseqc_innerdistance description: compare detected splice junctions to reference gene model keywords: - junctions - splicing - rnaseq tools: - rseqc: description: | RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: the alignment in bam format pattern: "*.{bam}" - bed: type: file description: a bed file for the reference gene model pattern: "*.{bed}" output: - bed: type: file description: bed file of annotated junctions pattern: "*.junction.bed" - interact_bed: type: file description: Interact bed file pattern: "*.Interact.bed" - xls: type: file description: xls file with junction information pattern: "*.xls" - pdf: type: file description: junction plot pattern: "*.junction.pdf" - events_pdf: type: file description: events plot pattern: "*.events.pdf" - rscript: type: file description: Rscript to reproduce the plots pattern: "*.r" - log: - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@drpatelh" - "@kevinmenden"