--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/commands_tests	Wed Mar 24 08:33:56 2021 +0000
@@ -0,0 +1,37 @@
+#commands to test the tools with "test_data" 
+
+ $ cd <path>/simtext
+
+ $ Rscript pubmed_by_queries.R --input "test-data/test_data" --output "test-data/pubmed_by_queries_output"
+ #output: test-data/pubmed_by_queries_output --install_packages
+
+ $ Rscript pubmed_by_queries.R --input "test-data/test_data" --abstract --output "test-data/pubmed_by_queries_output_abstracts" --install_packages
+ #output: test-data/pubmed_by_queries_output_abstracts
+
+ $ Rscript abstracts_by_pmids.R --input "test-data/pubmed_by_queries_output" --output "test-data/abstracts_by_pmids_output" --install_packages
+ #output: test-data/abstracts_by_pmids_output
+
+ $ Rscript text_to_wordmatrix.R --input "test-data/pubmed_by_queries_output_abstracts" --output "test-data/text_to_wordmatrix_output" --install_packages
+ #output: test-data/text_to_wordmatrix_output
+
+ $ 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
+ #output: test-data/text_to_wordmatrix_output_args
+ 
+  $ 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
+ #output: test-data/pmids_to_pubtator_matrix_output
+
+  $ 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
+ #output: test-data/pmids_to_pubtator_matrix_output_byid
+
+  $ 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
+ #output: test-data/pmids_to_pubtator_matrix_output_number
+
+ $ Rscript simtext_app.R -i "test-data/test_data" -m "test-data/text_to_wordmatrix_output" --install_packages
+ #output: ShinyApp
+
+ $ Rscript simtext_app.R -i "test-data/test_data" -m "test-data/pmids_to_pubtator_matrix_output" --install_packages
+ #output: ShinyApp
+
+
+
+