Mercurial > repos > dlalgroup > pmids_to_pubtator_matrix

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"planemo upload for repository https://github.com/dlal-group/simtext commit 63f67ee02be2eb4323a5ba5dcdd33d1fd0b7c24e"
author dlalgroup
date Thu, 08 Oct 2020 05:39:58 +0000
parents 3f4adc85ba5d
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3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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1 #commands to test the tools with "test_data"
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
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3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
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3 $ cd <path>/SimText/test
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
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3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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5 $ Rscript ../pubmed_by_queries.R --input "data/test_data" --output "data/pubmed_by_queries_output"
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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6 #output: data/pubmed_by_queries_output --install_packages
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
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3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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8 $ Rscript ../pubmed_by_queries.R --input "data/test_data" --abstract --output "data/pubmed_by_queries_output_abstracts" --install_packages
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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9 #output: data/pubmed_by_queries_output_abstracts
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
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3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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11 $ Rscript ../abstracts_by_pmids.R --input "data/pubmed_by_queries_output" --output "data/abstracts_by_pmids_output" --install_packages
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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12 #output: data/abstracts_by_pmids_output
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
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3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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14 $ Rscript ../text_to_wordmatrix.R --input "data/pubmed_by_queries_output_abstracts" --output "data/text_to_wordmatrix_output" --install_packages
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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15 #output: data/text_to_wordmatrix_output
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
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dlalgroup
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17 $ Rscript ../pmids_to_pubtator_matrix.R --input "data/pubmed_by_queries_output" --output "data/pmids_to_pubtator_matrix_output" --number 50 --install_packages
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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18 #output: data/pmids_to_pubtator_matrix_output
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
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3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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20 $ Rscript ../simtext_app.R -i "data/test_data" -m "data/text_to_wordmatrix_output" --install_packages
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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21 #output: ShinyApp
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
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23 $ Rscript ../simtext_app.R -i "data/test_data" -m "data/pmids_to_pubtator_matrix_output" --install_packages
3f4adc85ba5d "planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
dlalgroup
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24 #output: ShinyApp