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62 lines
1.7 KiB
YAML
62 lines
1.7 KiB
YAML
name: "hamronization_amrfinderplus"
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description: Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization specification.
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keywords:
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- amr
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- antimicrobial resistance
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- arg
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- antimicrobial resistance genes
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- reporting
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- amrfinderplus
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tools:
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- "hamronization":
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description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification"
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homepage: "https://github.com/pha4ge/hAMRonization/"
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documentation: "https://github.com/pha4ge/hAMRonization/"
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tool_dev_url: "https://github.com/pha4ge/hAMRonization"
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licence: "['GNU Lesser General Public v3 (LGPL v3)']"
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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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- report:
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type: file
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description: Output .tsv file from AMRfinderPlus
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pattern: "*.tsv"
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- format:
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type: value
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description: Type of report file to be produced
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pattern: "tsv|json"
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- software_version:
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type: value
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description: Version of AMRfinder used
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pattern: "[0-9].[0-9].[0-9]"
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- reference_db_version:
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type: value
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description: Database version of ncbi_AMRfinder used
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pattern: "[0-9]-[0-9]-[0-9].[0-9]"
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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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- json:
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type: file
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description: hAMRonised report in JSON format
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pattern: "*.json"
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- tsv:
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type: file
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description: hAMRonised report in TSV format
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pattern: "*.tsv"
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authors:
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- "@louperelo"
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