annotate examples/commands_examples @ 1:949e46ca234b draft default tip

"planemo upload for repository https://github.com/dlal-group/simtext commit fd3f5b7b0506fbc460f2a281f694cb57f1c90a3c-dirty"

#Commands to reproduce use-case examples


#### Use-case 1a #####

$ cd <path>/SimText

$ Rscript pubmed_by_queries.R \
 --input examples/data/1a/clingen_data \
 --output examples/data/1a/pubmed_by_queries_output \
 --number 500 \
 --abstract \
 --install_packages

$ Rscript text_to_wordmatrix.R \
 --input "examples/data/1a/pubmed_by_queries_output" \
 --output "examples/data/1a/clingen_data_matrix" \
 --number 100 \
 --install_packages

$ Rscript simtext_app.R \
 --input "examples/data/1a/clingen_data" \
 --matrix "examples/data/1a/clingen_data_matrix" \
 --install_packages



#### Use-case 1b #####

$ cd <path>/SimText

$ Rscript pubmed_by_queries.R \
 --input "examples/data/1b/clingen_data" \
 --output "examples/data/1b/pubmed_by_queries_output" \
 --number 500 \
 --install_packages

$ Rscript pmids_to_pubtator_matrix.R \
 --input "examples/data/1b/pubmed_by_queries_output"  \
 --output "examples/data/1b/clingen_data_matrix" \
 --categories Disease Gene \
 --number 100 \
 --install_packages

$ Rscript simtext_app.R \
 --input "examples/data/1b/clingen_data" \
 --matrix "examples/data/1b/clingen_data_matrix" \
 --install_packages


#### Use-case 2 #####

cd <path>/SimText

$ Rscript abstracts_by_pmids.R \
 --input "examples/data/2/researcher_data.txt" \
 --output "examples/data/2/abstracts_by_pmids_output"

$ Rscript text_to_wordmatrix.R \
 --input "examples/data/2/abstracts_by_pmids_output" \
 --output "examples/data/2/researcher_data_matrix" \
 --number 50

$ Rscript simtext_app.R \
 --input "examples/data/2/researcher_data.txt" \
 --matrix "examples/data/2/researcher_data_matrix"