Mercurial > repos > dlalgroup > pmids_to_pubtator_matrix
diff test/commands_tests @ 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 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/commands_tests Thu Sep 24 02:01:50 2020 +0000 @@ -0,0 +1,24 @@ +#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 \ No newline at end of file