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83 lines
3.2 KiB
YAML
83 lines
3.2 KiB
YAML
name: "vsearch_usearchglobal"
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description: Compare target sequences to fasta-formatted query sequences using global pairwise alignment.
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keywords:
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- vsearch
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- usearch
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- alignment
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- fasta
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tools:
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- "vsearch":
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description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)"
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homepage: "https://github.com/torognes/vsearch"
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documentation: "None"
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tool_dev_url: "https://github.com/torognes/vsearch"
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doi: "doi: 10.7717/peerj.2584"
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licence: "['GPL v3-or-later OR BSD-2-clause']"
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input:
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- meta:
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type: map
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description: Groovy Map containing sample information e.g. [ id:'test' ]
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- queryfasta:
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type: file
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description: Query sequences in FASTA format
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pattern: "*.{fasta,fa,fna,faa}"
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- db:
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type: file
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description: Reference database file in FASTA or UDB format
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pattern: "*"
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- idcutoff:
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type: real
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description: Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included)
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- outoption:
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type: string
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description: Specify the type of output file to be generated by selecting one of the vsearch output file options
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pattern: "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout"
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- user_columns:
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type: string
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description: If using the `userout` option, specify which columns to include in output, with fields separated with `+` (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string.
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output:
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- aln:
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type: file
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description: Results in pairwise alignment format
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pattern: "*.{aln}"
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- biom:
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type: file
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description: Results in an OTU table in the biom version 1.0 file format
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pattern: "*.{biom}"
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- lca:
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type: file
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description: Last common ancestor (LCA) information about the hits of each query in tab-separated format
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pattern: "*.{lca}"
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- mothur:
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type: file
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description: Results in an OTU table in the mothur ’shared’ tab-separated plain text file format
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pattern: "*.{mothur}"
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- otu:
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type: file
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description: Results in an OTU table in the classic tab-separated plain text format
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pattern: "*.{otu}"
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- sam:
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type: file
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description: Results written in sam format
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pattern: "*.{sam}"
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- tsv:
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type: file
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description: Results in tab-separated output, columns defined by user
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pattern: "*.{tsv}"
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- txt:
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type: file
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description: Tab delimited results in blast-like tabular format
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pattern: "*.{txt}"
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- uc:
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type: file
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description: Tab delimited results in a uclust-like format with 10 columns
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pattern: "*.{uc}"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@jtangrot"
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