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58 lines
1.9 KiB
YAML
Generated
58 lines
1.9 KiB
YAML
Generated
name: "taxpasta_merge"
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description: Standardise and merge two or more taxonomic profiles into a single table
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keywords:
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- taxonomic profile
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- standardise
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- standardisation
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- metagenomics
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- taxonomic profiling
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- otu tables
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- taxon tables
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tools:
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- "taxpasta":
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description: "TAXonomic Profile Aggregation and STAndardisation"
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homepage: "https://taxpasta.readthedocs.io/"
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documentation: "https://taxpasta.readthedocs.io/"
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tool_dev_url: "https://github.com/taxprofiler/taxpasta"
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licence: "['Apache-2.0']"
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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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- profiles:
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type: file
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description: A list of taxonomic profiler output files (typically in text format, mandatory)
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pattern: "*.{tsv,csv,arrow,parquet,biom}"
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- samplesheet:
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type: file
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description:
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A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative
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from the work environment. The profiles must be provided even if you give a samplesheet as argument (optional)
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pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet}"
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- taxonomy:
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type: directory
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description: Directory containing at a minimum nodes.dmp and names.dmp files (optional)
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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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- merged_profiles:
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type: file
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description: Output file with standardised multiple profiles in one go and have all profiles combined into a single table.
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pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}"
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authors:
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- "@sofstam"
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- "@jfy133"
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