Mercurial > repos > dlalgroup > pubmed_by_queries
comparison test/commands_tests @ 0:f40606281050 draft
"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
| author | dlalgroup |
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| date | Thu, 24 Sep 2020 03:01:43 +0000 |
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| children |
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| -1:000000000000 | 0:f40606281050 |
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| 1 #commands to test the tools with "test_data" | |
| 2 | |
| 3 $ cd <path>/SimText/test | |
| 4 | |
| 5 $ Rscript ../pubmed_by_queries.R --input "data/test_data" --output "data/pubmed_by_queries_output" | |
| 6 #output: data/pubmed_by_queries_output --install_packages | |
| 7 | |
| 8 $ Rscript ../pubmed_by_queries.R --input "data/test_data" --abstract --output "data/pubmed_by_queries_output_abstracts" --install_packages | |
| 9 #output: data/pubmed_by_queries_output_abstracts | |
| 10 | |
| 11 $ Rscript ../abstracts_by_pmids.R --input "data/pubmed_by_queries_output" --output "data/abstracts_by_pmids_output" --install_packages | |
| 12 #output: data/abstracts_by_pmids_output | |
| 13 | |
| 14 $ Rscript ../text_to_wordmatrix.R --input "data/pubmed_by_queries_output_abstracts" --output "data/text_to_wordmatrix_output" --install_packages | |
| 15 #output: data/text_to_wordmatrix_output | |
| 16 | |
| 17 $ Rscript ../pmids_to_pubtator_matrix.R --input "data/pubmed_by_queries_output" --output "data/pmids_to_pubtator_matrix_output" --number 50 --install_packages | |
| 18 #output: data/pmids_to_pubtator_matrix_output | |
| 19 | |
| 20 $ Rscript ../simtext_app.R -i "data/test_data" -m "data/text_to_wordmatrix_output" --install_packages | |
| 21 #output: ShinyApp | |
| 22 | |
| 23 $ Rscript ../simtext_app.R -i "data/test_data" -m "data/pmids_to_pubtator_matrix_output" --install_packages | |
| 24 #output: ShinyApp |