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f420d97ca2
* renamed output: xml * removed tail -n+3 from output * removed comment * removed blank space * removed blank space * updated test
57 lines
1.8 KiB
YAML
57 lines
1.8 KiB
YAML
name: "entrezdirect_esummary"
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description: Queries an NCBI database using Unique Identifier(s)
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keywords:
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- public datasets
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- ncbi
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- entrez
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- metadata
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- query
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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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- database:
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type: value
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description: Value must be a valid Entrez database name ('assembly', etc).
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- uid:
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type: value
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description: Unique Identifier (UID) of record in NCBI database. Cannot be used at the same time as uids_file
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- uids_file:
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type: file
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description: Text file containing multiple UIDs. Cannot be used at the same time as uid.
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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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- xml:
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type: file
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description: Query result in XML format
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pattern: "*.xml"
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authors:
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- "@alxndrdiaz"
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