Mercurial > repos > dlalgroup > pmids_to_pubtator_matrix
view examples/commands_examples @ 0:3f4adc85ba5d draft
"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
| author | dlalgroup |
|---|---|
| date | Thu, 24 Sep 2020 02:01:50 +0000 |
| parents | |
| children |
line wrap: on
line source
#Commands to reproduce use-case examples #### Use-case 1a ##### $ cd <path>/SimText $ Rscript pubmed_by_queries.R \ --input examples/data/1a/clingen_data \ --output examples/data/1a/pubmed_by_queries_output \ --number 500 \ --abstract \ --install_packages $ Rscript text_to_wordmatrix.R \ --input "examples/data/1a/pubmed_by_queries_output" \ --output "examples/data/1a/clingen_data_matrix" \ --number 100 \ --install_packages $ Rscript simtext_app.R \ --input "examples/data/1a/clingen_data" \ --matrix "examples/data/1a/clingen_data_matrix" \ --install_packages #### Use-case 1b ##### $ cd <path>/SimText $ Rscript pubmed_by_queries.R \ --input "examples/data/1b/clingen_data" \ --output "examples/data/1b/pubmed_by_queries_output" \ --number 500 \ --install_packages $ Rscript pmids_to_pubtator_matrix.R \ --input "examples/data/1b/pubmed_by_queries_output" \ --output "examples/data/1b/clingen_data_matrix" \ --categories Disease Gene \ --number 100 \ --install_packages $ Rscript simtext_app.R \ --input "examples/data/1b/clingen_data" \ --matrix "examples/data/1b/clingen_data_matrix" \ --install_packages #### Use-case 2 ##### cd <path>/SimText $ Rscript abstracts_by_pmids.R \ --input "examples/data/2/researcher_data.txt" \ --output "examples/data/2/abstracts_by_pmids_output" $ Rscript text_to_wordmatrix.R \ --input "examples/data/2/abstracts_by_pmids_output" \ --output "examples/data/2/researcher_data_matrix" \ --number 50 $ Rscript simtext_app.R \ --input "examples/data/2/researcher_data.txt" \ --matrix "examples/data/2/researcher_data_matrix"