mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 19:19:54 +00:00
59 lines
1.9 KiB
YAML
59 lines
1.9 KiB
YAML
|
name: "taxpasta_merge"
|
||
|
|
description: Standardise and merge two or more taxonomic profiles into a single table
|
||
|
|
keywords:
|
||
|
|
- taxonomic profile
|
||
|
|
- standardise
|
||
|
|
- standardisation
|
||
|
|
- metagenomics
|
||
|
|
- taxonomic profiling
|
||
|
|
- otu tables
|
||
|
|
- taxon tables
|
||
|
|
tools:
|
||
|
|
- "taxpasta":
|
||
|
|
description: "TAXonomic Profile Aggregation and STAndardisation"
|
||
|
|
homepage: "https://taxpasta.readthedocs.io/"
|
||
|
|
documentation: "https://taxpasta.readthedocs.io/"
|
||
|
|
tool_dev_url: "https://github.com/taxprofiler/taxpasta"
|
||
|
|
doi: ""
|
||
|
|
licence: "['Apache-2.0']"
|
||
|
|
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- profiles:
|
||
|
|
type: file
|
||
|
|
description: A list of taxonomic profiler output files (typically in text format, mandatory)
|
||
|
|
pattern: "*.{tsv,csv,arrow,parquet,biom}"
|
||
|
|
- samplesheet:
|
||
|
|
type: file
|
||
|
|
description:
|
||
|
|
A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative
|
||
|
|
from the work environment. The profiles must be provided even if you give a samplesheet as argument (optional)
|
||
|
|
pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet}"
|
||
|
|
- taxonomy:
|
||
|
|
type: directory
|
||
|
|
description: Directory containing at a minimum nodes.dmp and names.dmp files (optional)
|
||
|
|
pattern: "*/"
|
||
|
|
|
||
|
|
output:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- versions:
|
||
|
|
type: file
|
||
|
|
description: File containing software versions
|
||
|
|
pattern: "versions.yml"
|
||
|
|
- merged_profiles:
|
||
|
|
type: file
|
||
|
|
description: Output file with standardised multiple profiles in one go and have all profiles combined into a single table.
|
||
|
|
pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}"
|
||
|
|
|
||
|
|
authors:
|
||
|
|
- "@sofstam"
|
||
|
|
- "@jfy133"
|