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46 lines
1.3 KiB
YAML
46 lines
1.3 KiB
YAML
name: hamronization_summarize
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description: Tool to summarize and combine all hAMRonization reports into a single file
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keywords:
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- amr
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- antimicrobial resistance
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- reporting
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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/blob/master/README.md
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documentation: https://github.com/pha4ge/hAMRonization/blob/master/README.md
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tool_dev_url: https://github.com/pha4ge/hAMRonization
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doi: ""
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licence: ["GNU Lesser General Public v3 (LGPL v3)"]
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input:
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- reports:
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type: file
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description: List of multiple hAMRonization reports in either JSON or TSV format
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pattern: "*.{json,tsv}"
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- format:
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type: value
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description: Type of final combined report file to be produced
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pattern: "tsv|json|interactive"
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output:
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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 summary 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 summary in TSV format
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pattern: "*.json"
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- html:
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type: file
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description: hAMRonised summary in HTML format
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pattern: "*.html"
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authors:
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- "@jfy133"
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