jvarkit

PubmedFilterJS

Last commit

Filters Pubmed XML with a javascript (java rhino) expression. Context contain ‘article’ a PubmedBookArticle or a PubmedArticle and ‘index’, the index in the XML file.

Usage

Usage: pubmedfilterjs [options] Files
  Options:
    -e, --expression
      Javascript expression
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --output
      Output file. Optional . Default: stdout
    -f, --scriptfile
      Javascript file
    --version
      print version and exit

Keywords

Compilation

Requirements / Dependencies

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew pubmedfilterjs

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/pubmed/PubmedFilterJS.java

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License

The project is licensed under the MIT license.

Citing

Should you cite pubmedfilterjs ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030