Mercurial > repos > mgramm > abstracts_by_pmids
view test/commands_tests @ 0:01f691e9ba03 draft default tip
"planemo upload for repository https://github.com/dlal-group/simtext commit e55e96337165eebd0e2b365bcd0ae48ebb358ebc-dirty"
author | mgramm |
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date | Thu, 03 Sep 2020 14:49:19 +0000 |
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#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