annotate test/commands_tests @ 1:882780a04b8d draft default tip

"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"

#commands to test the tools with "test_data" 

 $ cd <path>/SimText/test

 $ Rscript ../pubmed_by_queries.R --input "data/test_data" --output "data/pubmed_by_queries_output"
 #output: data/pubmed_by_queries_output --install_packages

 $ Rscript ../pubmed_by_queries.R --input "data/test_data" --abstract --output "data/pubmed_by_queries_output_abstracts" --install_packages
 #output: data/pubmed_by_queries_output_abstracts

 $ Rscript ../abstracts_by_pmids.R --input "data/pubmed_by_queries_output" --output "data/abstracts_by_pmids_output" --install_packages
 #output: data/abstracts_by_pmids_output

 $ Rscript ../text_to_wordmatrix.R --input "data/pubmed_by_queries_output_abstracts" --output "data/text_to_wordmatrix_output" --install_packages
 #output: data/text_to_wordmatrix_output
 
  $ Rscript ../pmids_to_pubtator_matrix.R --input "data/pubmed_by_queries_output" --output "data/pmids_to_pubtator_matrix_output" --number 50 --install_packages
 #output: data/pmids_to_pubtator_matrix_output

 $ Rscript ../simtext_app.R -i "data/test_data" -m "data/text_to_wordmatrix_output" --install_packages
 #output: ShinyApp

 $ Rscript ../simtext_app.R -i "data/test_data" -m "data/pmids_to_pubtator_matrix_output" --install_packages
 #output: ShinyApp