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annotate examples/commands_examples @ 0:d7aea8ba1e30 draft

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"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"
author dlalgroup
date Thu, 24 Sep 2020 03:11:08 +0000
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1 #Commands to reproduce use-case examples
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4 #### Use-case 1a #####
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6 $ cd <path>/SimText
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8 $ Rscript pubmed_by_queries.R \
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9 --input examples/data/1a/clingen_data \
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10 --output examples/data/1a/pubmed_by_queries_output \
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11 --number 500 \
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12 --abstract \
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13 --install_packages
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15 $ Rscript text_to_wordmatrix.R \
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16 --input "examples/data/1a/pubmed_by_queries_output" \
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17 --output "examples/data/1a/clingen_data_matrix" \
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18 --number 100 \
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19 --install_packages
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21 $ Rscript simtext_app.R \
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22 --input "examples/data/1a/clingen_data" \
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23 --matrix "examples/data/1a/clingen_data_matrix" \
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24 --install_packages
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28 #### Use-case 1b #####
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30 $ cd <path>/SimText
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32 $ Rscript pubmed_by_queries.R \
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33 --input "examples/data/1b/clingen_data" \
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34 --output "examples/data/1b/pubmed_by_queries_output" \
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35 --number 500 \
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36 --install_packages
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38 $ Rscript pmids_to_pubtator_matrix.R \
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39 --input "examples/data/1b/pubmed_by_queries_output" \
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40 --output "examples/data/1b/clingen_data_matrix" \
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41 --categories Disease Gene \
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42 --number 100 \
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43 --install_packages
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45 $ Rscript simtext_app.R \
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46 --input "examples/data/1b/clingen_data" \
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47 --matrix "examples/data/1b/clingen_data_matrix" \
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48 --install_packages
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51 #### Use-case 2 #####
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53 cd <path>/SimText
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55 $ Rscript abstracts_by_pmids.R \
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56 --input "examples/data/2/researcher_data.txt" \
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57 --output "examples/data/2/abstracts_by_pmids_output"
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59 $ Rscript text_to_wordmatrix.R \
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60 --input "examples/data/2/abstracts_by_pmids_output" \
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61 --output "examples/data/2/researcher_data_matrix" \
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62 --number 50
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64 $ Rscript simtext_app.R \
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65 --input "examples/data/2/researcher_data.txt" \
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66 --matrix "examples/data/2/researcher_data_matrix"
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