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comparison examples/commands_examples @ 0:34ed44f3f85c 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 02:17:05 +0000
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1 #Commands to reproduce use-case examples
2
3
4 #### Use-case 1a #####
5
6 $ cd <path>/SimText
7
8 $ Rscript pubmed_by_queries.R \
9 --input examples/data/1a/clingen_data \
10 --output examples/data/1a/pubmed_by_queries_output \
11 --number 500 \
12 --abstract \
13 --install_packages
14
15 $ Rscript text_to_wordmatrix.R \
16 --input "examples/data/1a/pubmed_by_queries_output" \
17 --output "examples/data/1a/clingen_data_matrix" \
18 --number 100 \
19 --install_packages
20
21 $ Rscript simtext_app.R \
22 --input "examples/data/1a/clingen_data" \
23 --matrix "examples/data/1a/clingen_data_matrix" \
24 --install_packages
25
26
27
28 #### Use-case 1b #####
29
30 $ cd <path>/SimText
31
32 $ Rscript pubmed_by_queries.R \
33 --input "examples/data/1b/clingen_data" \
34 --output "examples/data/1b/pubmed_by_queries_output" \
35 --number 500 \
36 --install_packages
37
38 $ Rscript pmids_to_pubtator_matrix.R \
39 --input "examples/data/1b/pubmed_by_queries_output" \
40 --output "examples/data/1b/clingen_data_matrix" \
41 --categories Disease Gene \
42 --number 100 \
43 --install_packages
44
45 $ Rscript simtext_app.R \
46 --input "examples/data/1b/clingen_data" \
47 --matrix "examples/data/1b/clingen_data_matrix" \
48 --install_packages
49
50
51 #### Use-case 2 #####
52
53 cd <path>/SimText
54
55 $ Rscript abstracts_by_pmids.R \
56 --input "examples/data/2/researcher_data.txt" \
57 --output "examples/data/2/abstracts_by_pmids_output"
58
59 $ Rscript text_to_wordmatrix.R \
60 --input "examples/data/2/abstracts_by_pmids_output" \
61 --output "examples/data/2/researcher_data_matrix" \
62 --number 50
63
64 $ Rscript simtext_app.R \
65 --input "examples/data/2/researcher_data.txt" \
66 --matrix "examples/data/2/researcher_data_matrix"
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