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b4452a4881
* first commit * entrezdirect/esummary fixed version definition * resolved suggestion * updated main.nf * changed output definition * output: XML file * output definition: XML file * updated XML format in tests * updated test file * version: esummary instead of entrezdirect * output file pattern: *.esummary.xml * updated test file * updated versions * restored versions stdout * updated test file * changed xml_esummary pattern * changed entrezdirect to esummary version * updated test file * Update modules/entrezdirect/esummary/meta.yml changed output file pattern: "*.xml" Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/meta.yml updated keywords Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf Output file pattern: *.xml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf Output file pattern: *.xml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf database as separate input channel Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * removed blank spaces in input definition * database as separate channel * conditional script for stdin * updated input definition * entrez-direct version:16.2_1 * all input channels are separate * ignore stderr, catch xml stdout * removed blank lines * added ids file input * updated test * conditional script for input * removed bad definition of input file * updated test file * Update modules/entrezdirect/esummary/main.nf changed input definition: ui, uids_file Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/meta.yml added uids_file description Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/entrezdirect/esummary/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * input: uid or uids_file * updated input * added uids_file to input * input file as optional input * input file as optional input in each test * new conditional script * unpdated test file * single input definition * added error messages * updated test * removed cat from command output * Update modules/entrezdirect/esummary/main.nf added comment on use of grep in output Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added comment * removed blank spaces * input file: empty list * input file: empty list * removed comment at wrong position * optional file defined as empty list * updated successful test * Apply suggestions from code review Accepted suggestions. Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * Update modules/entrezdirect/esummary/main.nf Fixed comment. Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * Update modules/entrezdirect/esummary/main.nf Updated grep in output file. Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> * added tail -n+3 before output * updated successful test Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
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_esummary:
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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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