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4ed5dc4593
* added module files * latest version * latest version * latest version * latest version * updated test, failing * added comment on why to use tail -n+3 * same as latest test * moved args to the end of script * updated test * double quotes for esearch input * removed tail -n+3, stderr is redirected by nextflow * changed single to double quotes * Update modules/entrezdirect/esearch/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esearch/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update meta.yml removed default from database parameter Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
55 lines
1.6 KiB
YAML
55 lines
1.6 KiB
YAML
name: "entrezdirect_esearch"
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description: Searches a term in a public NCBI database
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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' ]
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- database:
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type: value
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description: Value must be a valid Entrez database name.
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- term:
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type: value
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description: |
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Entrez text query. All special characters must be URL encoded.
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Spaces may be replaced by '+' signs.
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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' ]
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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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- result_xml:
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type: file
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description: Query result text in XML format
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pattern: "*.xml"
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authors:
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- "@alxndrdiaz"
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