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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 08:30:44 +0000
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6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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1 #commands to test the tools with "test_data"
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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3 $ cd <path>/simtext
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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5 $ Rscript pubmed_by_queries.R --input "test-data/test_data" --output "test-data/pubmed_by_queries_output"
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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6 #output: test-data/pubmed_by_queries_output --install_packages
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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8 $ Rscript pubmed_by_queries.R --input "test-data/test_data" --abstract --output "test-data/pubmed_by_queries_output_abstracts" --install_packages
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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9 #output: test-data/pubmed_by_queries_output_abstracts
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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11 $ Rscript abstracts_by_pmids.R --input "test-data/pubmed_by_queries_output" --output "test-data/abstracts_by_pmids_output" --install_packages
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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12 #output: test-data/abstracts_by_pmids_output
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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14 $ Rscript text_to_wordmatrix.R --input "test-data/pubmed_by_queries_output_abstracts" --output "test-data/text_to_wordmatrix_output" --install_packages
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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15 #output: test-data/text_to_wordmatrix_output
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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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
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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18 #output: test-data/text_to_wordmatrix_output_args
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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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
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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21 #output: test-data/pmids_to_pubtator_matrix_output
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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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
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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24 #output: test-data/pmids_to_pubtator_matrix_output_byid
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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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
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
iuc
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27 #output: test-data/pmids_to_pubtator_matrix_output_number
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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29 $ Rscript simtext_app.R -i "test-data/test_data" -m "test-data/text_to_wordmatrix_output" --install_packages
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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30 #output: ShinyApp
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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32 $ Rscript simtext_app.R -i "test-data/test_data" -m "test-data/pmids_to_pubtator_matrix_output" --install_packages
6cf106b8916f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/simtext commit 63a5e13cf89cdd209d20749c582ec5b8dde4e208"
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33 #output: ShinyApp
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