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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>
61 lines
2 KiB
YAML
61 lines
2 KiB
YAML
name: macrel_contigs
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description: A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.
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keywords:
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- AMP
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- antimicrobial peptides
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- genome mining
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- metagenomes
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- peptide prediction
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tools:
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- macrel:
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description: A pipeline for AMP (antimicrobial peptide) prediction
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homepage: https://macrel.readthedocs.io/en/latest/
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documentation: https://macrel.readthedocs.io/en/latest/
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tool_dev_url: https://github.com/BigDataBiology/macrel
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doi: "10.7717/peerj.10555"
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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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- fasta:
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type: file
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description: A fasta file with nucleotide sequences.
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pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}"
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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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- amp_prediction:
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type: file
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description: A zipped file, with all predicted amps in a table format.
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pattern: "*.prediction.gz"
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- smorfs:
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type: file
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description: A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs.
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pattern: "*.smorfs.faa.gz"
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- all_orfs:
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type: file
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description: A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs.
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pattern: "*.all_orfs.faa.gz"
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- readme_file:
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type: file
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description: A readme file containing tool specific information (e.g. citations, details about the output, etc.).
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pattern: "*.md"
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- log_file:
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type: file
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description: A log file containing the information pertaining to the run.
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pattern: "*_log.txt"
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authors:
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- "@darcy220606"
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