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37c6d4a1a1
* first commit
* single taxon input
* added .tsv output
* input: single taxon or file with taxon identifiers
* updated input and output
* removed wrong tool description
* added tests
* ext.args = '-l -b'
* fixed wrong input names
* updated test file
* Update modules/goat/taxonsearch/main.nf
simple version output
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* removed 'NO_FILE' from input definition
* added ! in if statement
* optional input: empty list
* successful updated test
* added test with file
* remove blank spaces in include {}
* added test with taxa file
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
51 lines
1.4 KiB
YAML
51 lines
1.4 KiB
YAML
name: "goat_taxonsearch"
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description: Query metadata for any taxon across the tree of life.
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keywords:
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- public datasets
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- ncbi
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- genomes on a tree
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tools:
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- goat:
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description: |
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goat-cli is a command line interface to query the
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Genomes on a Tree Open API.
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homepage: https://github.com/genomehubs/goat-cli
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documentation: https://github.com/genomehubs/goat-cli/wiki
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tool_dev_url: https://genomehubs.github.io/goat-cli/goat_cli/
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doi: "None"
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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']
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- taxon:
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type: val
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description: |
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The taxon to search. An NCBI taxon ID, or the name of a taxon at any rank.
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- taxa_file:
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type: file
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description: |
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A file of NCBI taxonomy ID's (tips) and/or binomial names. Each line
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should contain a single entry.File size is limited to 500 entries.
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pattern: "*.txt"
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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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- taxonsearch:
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type: file
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description: TSV file containing search results.
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pattern: "*.tsv"
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authors:
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- "@alxndrdiaz"
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