annotate test/commands_tests @ 0:69714f06f18b draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"

#commands to test the tools with "test_data" 

 $ cd <path>/simtext

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

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

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

 $ Rscript text_to_wordmatrix.R --input "test-data/pubmed_by_queries_output_abstracts" --output "test-data/text_to_wordmatrix_output" --install_packages
 #output: test-data/text_to_wordmatrix_output

 $ Rscript text_to_wordmatrix.R --input "test-data/pubmed_by_queries_output_abstracts" --output "test-data/text_to_wordmatrix_output_args" --remove_num --remove_stopwords --plurals --install_packages
 #output: test-data/text_to_wordmatrix_output_args
 
  $ Rscript test-data/pmids_to_pubtator_matrix.R --input "test-data/pubmed_by_queries_output" --output "test-datadata/pmids_to_pubtator_matrix_output" --number 50 --categories Gene Mutation --install_packages
 #output: test-data/pmids_to_pubtator_matrix_output

  $ Rscript pmids_to_pubtator_matrix.R --input "test-data/pubmed_by_queries_output" --output "test-data/pmids_to_pubtator_matrix_output_byid" --number 50 --categories Gene Disease --install_packages --byid
 #output: test-data/pmids_to_pubtator_matrix_output_byid

  $ Rscript pmids_to_pubtator_matrix.R --input "test-data/pubmed_by_queries_output" --output "test-data/pmids_to_pubtator_matrix_output_number" --number 5 --categories Gene Disease --install_packages
 #output: test-data/pmids_to_pubtator_matrix_output_number

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

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