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c3bacb9fdd
* Add deeparg download data * Tweak downloaddata test.yml * Add deeparg tests * Apply suggestions from code review * Fix output file paths in test * Fix tests again md5sum to string
68 lines
2.1 KiB
YAML
68 lines
2.1 KiB
YAML
name: deeparg_predict
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description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
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keywords:
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- deeparg
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- antimicrobial resistance
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- antimicrobial resistance genes
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- arg
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- deep learning
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- prediction
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- contigs
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- metagenomes
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tools:
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- deeparg:
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description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes
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homepage: https://bench.cs.vt.edu/deeparg
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documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
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tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/
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doi: "10.1186/s40168-018-0401-z"
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licence: ['MIT']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- fasta:
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type: file
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description: FASTA file containing gene-like sequences
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pattern: "*.{fasta,fa,fna}"
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- model:
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type: string
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description: Which model to use, depending on input data. Either 'LS' or 'SS' for long or short sequences respectively
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pattern: "LS|LS"
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- db:
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type: directory
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description: Path to a directory containing the deepARG pre-built models
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pattern: "*/"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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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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- daa:
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type: file
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description: Sequences of ARG-like sequences from DIAMOND alignment
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pattern: "*.align.daa"
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- daa_tsv:
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type: file
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description: Alignments scores against ARG-like sequences from DIAMOND alignment
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pattern: "*.align.daa.tsv"
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- arg:
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type: file
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description: Table containing sequences with an ARG-like probability of more than specified thresholds
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pattern: "*.mapping.ARG"
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- potential_arg:
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type: file
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description: Table containing sequences with an ARG-like probability of less than specified thresholds, and requires manual inspection
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pattern: "*.mapping.potential.ARG"
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authors:
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- "@jfy133"
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