Mercurial > repos > mingchen0919 > elastic_expose_data
changeset 4:9ff33a3631fa draft
planemo upload commit 979e0f1c28c74ca7df02ef20c2208e9677bc820a-dirty
| author | mingchen0919 |
|---|---|
| date | Mon, 02 Apr 2018 08:32:59 -0400 |
| parents | 5838300fc1aa |
| children | 4f9f1e76f7e6 |
| files | elastic_expose_individuals.xml elastic_expose_to_list_collection.xml elastic_expose_to_list_paired_collection.xml individuals.Rmd individuals_render.R |
| diffstat | 5 files changed, 17 insertions(+), 11 deletions(-) [+] |
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--- a/elastic_expose_individuals.xml Mon Apr 02 00:32:04 2018 -0400 +++ b/elastic_expose_individuals.xml Mon Apr 02 08:32:59 2018 -0400 @@ -51,7 +51,7 @@ ############ run render R script to render R markdowns - Rscript '${__tool_directory__}/paired_render.R' + Rscript '${__tool_directory__}/individuals_render.R' ]]></command> <inputs> @@ -61,11 +61,10 @@ </repeat> </inputs> <outputs> - <data format="html" name="report" label="${tool.name} report"/> - <data format="txt" name="tool_log" label="${tool.name} log"/> - <data name="individual_outputs"> + <data format="html" name="report" label="${tool.name} report ${on_string}"> <discover_datasets pattern="__designation_and_ext__" directory="individual_outputs" visible="true"/> </data> + <data format="txt" name="tool_log" label="${tool.name} log ${on_string}"/> </outputs> <citations> <expand macro="citations"/>
--- a/elastic_expose_to_list_collection.xml Mon Apr 02 00:32:04 2018 -0400 +++ b/elastic_expose_to_list_collection.xml Mon Apr 02 08:32:59 2018 -0400 @@ -61,8 +61,8 @@ </repeat> </inputs> <outputs> - <data format="html" name="report" label="${tool.name} report"/> - <data format="txt" name="tool_log" label="${tool.name} log"/> + <data format="html" name="report" label="${tool.name} report ${on_string}"/> + <data format="txt" name="tool_log" label="${tool.name} log ${on_string}"/> <collection type="list" name="list_collection"> <discover_datasets pattern="__name_and_ext__" directory="list" /> </collection>
--- a/elastic_expose_to_list_paired_collection.xml Mon Apr 02 00:32:04 2018 -0400 +++ b/elastic_expose_to_list_paired_collection.xml Mon Apr 02 08:32:59 2018 -0400 @@ -61,8 +61,8 @@ </repeat> </inputs> <outputs> - <data format="html" name="report" label="${tool.name} report"/> - <data format="txt" name="tool_log" label="${tool.name} log"/> + <data format="html" name="report" label="${tool.name} report ${on_string}"/> + <data format="txt" name="tool_log" label="${tool.name} log ${on_string}"/> <collection type="list:paired" name="list_paired_collection"> <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" directory="list_paired"/> </collection>
--- a/individuals.Rmd Mon Apr 02 00:32:04 2018 -0400 +++ b/individuals.Rmd Mon Apr 02 08:32:59 2018 -0400 @@ -37,11 +37,15 @@ full_path = paste0(tool_output_dir, '/', df[i, 'relative_path']) if (dir.exists(full_path)) { from_files = list.files(full_path, full.names = TRUE) - to_files = paste0(Sys.getenv('individual_outputs/'), list.files(full_path)) + to_files = list.files(full_path) + to_files = paste0(individual_outputs_path, to_files) file.copy(from = from_files, to = to_files) } if (file.exists(full_path)) { - file.copy(from = full_path, to = paste0(Sys.getenv('individual_outputs/'), df[i, 'relative_path'])) + # to_files = list.files(full_path) + to_file = tail(strsplit(full_path, '/')[[1]], 1) + print(to_file) + file.copy(from = full_path, to = paste0(individual_outputs_path, to_file)) } # command_line = paste0('cp -r ', full_path, ' paired') # write(command_line, append = TRUE,
--- a/individuals_render.R Mon Apr 02 00:32:04 2018 -0400 +++ b/individuals_render.R Mon Apr 02 08:32:59 2018 -0400 @@ -19,9 +19,12 @@ # create three folders within working directory dir.create('individual_outputs') +job_working_dir = getwd() +individual_outputs_path = paste0(job_working_dir, '/individual_outputs/') + #-----------------render Rmd-------------- # copy R markdown file to working directory and render it within the working directory. -render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/paired.Rmd'), +render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/individuals.Rmd'), output_file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/report.html')) # for some unknow reason, directly using REPORT as the input value for output_file parameter