name: bamtools_convert description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. keywords: - bamtools - bamtools/convert - bam - convert - bed - fasta - fastq - json - pileup - sam - yaml tools: - bamtools: description: C++ API & command-line toolkit for working with BAM data homepage: http://github.com/pezmaster31/bamtools documentation: https://github.com/pezmaster31/bamtools/wiki tool_dev_url: http://github.com/pezmaster31/bamtools doi: "" licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM file pattern: "*.bam" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - out: type: file description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml) pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}" authors: - "@sguizard"