name: metaphlan3 description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. keywords: - metagenomics - classification - fastq - bam - fasta tools: - metaphlan3: description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.7554/eLife.65088" licence: ["MIT License"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - input: type: file description: Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out) pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" 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" - profile: type: file description: Tab-separated output file of the predicted taxon relative abundances pattern: "*.{txt}" - biom: type: file description: General-use format for representing biological sample by observation contingency tables pattern: "*.{biom}" - bowtie2out: type: file description: Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 ) pattern: "*.{bowtie2out.txt}" authors: - "@MGordon09"