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* first commit: module files * last version main.nf * modules/entrezdirect/xtract/meta.yml * updated file * updated test * Update modules/entrezdirect/xtract/main.nf changed name of output file Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/xtract/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tests/modules/entrezdirect/xtract/main.nf Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * Update tests/modules/entrezdirect/xtract/main.nf Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * updated test, removed esummary input file Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
59 lines
1.8 KiB
YAML
59 lines
1.8 KiB
YAML
name: "entrezdirect_xtract"
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description: Queries an NCBI database using an UID
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keywords:
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- public datasets
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- entrez
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- search
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- ncbi
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- database
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tools:
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- entrezdirect:
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description: |
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Entrez Direct (EDirect) is a method for accessing the NCBI's set of
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interconnected databases (publication, sequence, structure, gene,
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variation, expression, etc.) from a UNIX terminal window. Functions
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take search terms from command line arguments. Individual operations
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are combined to build multi-step queries. Record retrieval and
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formatting normally complete the process.
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homepage: https://www.ncbi.nlm.nih.gov/books/NBK179288/
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documentation: https://www.ncbi.nlm.nih.gov/books/NBK25501/
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tool_dev_url: https://www.ncbi.nlm.nih.gov/books/NBK25498/
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doi: 10.1016/S0076-6879(96)66012-1
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licence: ["PUBLIC DOMAIN"]
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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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- xml_input:
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type: file
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description: XML text file containing query results from database.
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- pattern:
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type: value
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description: String in xml_input that encloses element to search.
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- element:
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type: value
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description: Space-delimited strings that will be converted to columns.
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- sep:
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type: value
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description: Separator/delimiter between columns (for instance "," or "\t").
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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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- xtract_table:
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type: file
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description: TXT file containing columns searched from element.
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pattern: "*.txt"
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authors:
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- "@alxndrdiaz"
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