Mercurial > repos > iuc > pubmed_by_queries

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
author iuc
date Wed, 24 Mar 2021 08:34:22 +0000
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1 #commands to test the tools with "test_data"
2
3 $ cd <path>/simtext
4
5 $ Rscript pubmed_by_queries.R --input "test-data/test_data" --output "test-data/pubmed_by_queries_output"
6 #output: test-data/pubmed_by_queries_output --install_packages
7
8 $ Rscript pubmed_by_queries.R --input "test-data/test_data" --abstract --output "test-data/pubmed_by_queries_output_abstracts" --install_packages
9 #output: test-data/pubmed_by_queries_output_abstracts
10
11 $ Rscript abstracts_by_pmids.R --input "test-data/pubmed_by_queries_output" --output "test-data/abstracts_by_pmids_output" --install_packages
12 #output: test-data/abstracts_by_pmids_output
13
14 $ Rscript text_to_wordmatrix.R --input "test-data/pubmed_by_queries_output_abstracts" --output "test-data/text_to_wordmatrix_output" --install_packages
15 #output: test-data/text_to_wordmatrix_output
16
17 $ 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
18 #output: test-data/text_to_wordmatrix_output_args
19
20 $ 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
21 #output: test-data/pmids_to_pubtator_matrix_output
22
23 $ 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
24 #output: test-data/pmids_to_pubtator_matrix_output_byid
25
26 $ 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
27 #output: test-data/pmids_to_pubtator_matrix_output_number
28
29 $ Rscript simtext_app.R -i "test-data/test_data" -m "test-data/text_to_wordmatrix_output" --install_packages
30 #output: ShinyApp
31
32 $ Rscript simtext_app.R -i "test-data/test_data" -m "test-data/pmids_to_pubtator_matrix_output" --install_packages
33 #output: ShinyApp
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