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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
100 lines
3.6 KiB
YAML
100 lines
3.6 KiB
YAML
name: fargene
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description: tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output.
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keywords:
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- antibiotic resistance genes
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- ARGs
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- identifier
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- metagenomic
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- contigs
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tools:
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- fargene:
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description: Fragmented Antibiotic Resistance Gene Identifier takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output
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homepage: https://github.com/fannyhb/fargene
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documentation: https://github.com/fannyhb/fargene
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tool_dev_url: https://github.com/fannyhb/fargene
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doi: ""
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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', single_end:false ]
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- input:
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type: file
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description: uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq)
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pattern: "*.{fasta}"
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- hmm_model:
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type: string
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description: name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme]
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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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- log:
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type: file
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description: log file
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pattern: "*.{log}"
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- txt:
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type: file
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description: analysis summary text file
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pattern: "*.{txt}"
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- hmm:
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type: file
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description: output from hmmsearch
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pattern: "*.{out}"
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- orfs:
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type: file
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description: open reading frames (ORFs)
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pattern: "*.{fasta}"
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- orfs_amino:
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type: file
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description: protein translation of open reading frames (ORFs)
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pattern: "*.{fasta}"
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- contigs:
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type: file
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description: (complete) contigs that passed the final full-length classification
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pattern: "*.{fasta}"
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- contigs_pept:
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type: file
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description: parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences
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pattern: "*.{fasta}"
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- filtered:
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type: file
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description: sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene
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pattern: "*.{fasta}"
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- filtered_pept:
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type: file
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description: sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located
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pattern: "*.{fasta}"
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- fragments:
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type: file
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description: All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files
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pattern: "*.{fastq}"
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- trimmed:
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type: file
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description: The quality controlled retrieved fragments from each input file.
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pattern: "*.{fasta}"
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- spades:
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type: directory
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description: The output from the SPAdes assembly
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pattern: "spades_assembly"
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- metagenome:
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type: file
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description: The FASTQ to FASTA converted input files from metagenomic reads.
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pattern: "*.{fasta}"
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- tmp:
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type: file
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description: The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used.
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pattern: "*.{fasta}"
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authors:
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- "@louperelo"
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