Mercurial > repos > mingchen0919 > elastic_expose_data
changeset 2:391394c022b8 draft
planemo upload commit dd293cd7bf2d71c81f268b67bac8add01ec6df0a-dirty
| author | mingchen0919 |
|---|---|
| date | Sat, 31 Mar 2018 21:32:17 -0400 |
| parents | 16e0f4b7a286 |
| children | 5838300fc1aa |
| files | elastic_expose_to_list_collection.xml elastic_expose_to_list_paired_collection.xml elastic_expose_to_paired_collection.xml elastic_tool_wrappers_macros.xml list.Rmd list_paired.Rmd list_paired_render.R list_render.R paired.Rmd paired_render.R |
| diffstat | 10 files changed, 283 insertions(+), 69 deletions(-) [+] |
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--- a/elastic_expose_to_list_collection.xml Mon Mar 26 18:40:39 2018 -0400 +++ b/elastic_expose_to_list_collection.xml Sat Mar 31 21:32:17 2018 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="elastic_expose_to_list_collection" name="expose to a list" version="1.0.0"> +<tool id="elastic_expose_to_list_collection" name="expose data (list)" version="1.0.0"> <macros> <import>elastic_tool_wrappers_macros.xml</import> </macros> @@ -8,9 +8,57 @@ <expand macro="rmarkdown_requirements"/> </requirements> <expand macro="stdio"/> - <expand macro="shell_command"/> + <command><![CDATA[ + + ############ first, create a directory to store all files + mkdir -p $report.files_path && + + + ############ save the tool installation directory to an environment variable + export TOOL_INSTALL_DIR='${__tool_directory__}' && + + + ######################### + ## + ## save user input option/argument pairs into a file + ## + ######################### + + ## first line will be the header + echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' && + + + + #################################################### + ## loop through repeats to get option/argument pairs + #################################################### + + + ############ option_argument_path_relative_to_a_tool + #for i in $option_argument_path_relative_to_a_tool_repeat: + #set $item = str($i.a_tool_output_dir) + "|" + str($i.value) + echo '$item' >> '$report.files_path/options_and_arguments.txt' && + #end for + + + ############ output_set + ## '$report' + ## '$report.files_path' + ####################### + export REPORT='$report' && + export TOOL_LOG='$tool_log' && + export REPORT_FILES_PATH='$report.files_path' && + + + ############ run render R script to render R markdowns + Rscript '${__tool_directory__}/list_render.R' + + ]]></command> <inputs> - <expand macro="option_argument_path_relative_to_a_tool"/> + <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="0" default="0"> + <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/> + <param type="text" name="value" optional="true" label="relative path"/> + </repeat> </inputs> <outputs> <data format="html" name="report" label="${tool.name} report"/>
--- a/elastic_expose_to_list_paired_collection.xml Mon Mar 26 18:40:39 2018 -0400 +++ b/elastic_expose_to_list_paired_collection.xml Sat Mar 31 21:32:17 2018 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="elastic_expose_to_paired_collection" name="elastic_expose_to_paired_collection" version="1.0.0"> +<tool id="elastic_expose_to_paired_collection" name="expose data (list:paired)" version="1.0.0"> <macros> <import>elastic_tool_wrappers_macros.xml</import> </macros> @@ -8,16 +8,63 @@ <expand macro="rmarkdown_requirements"/> </requirements> <expand macro="stdio"/> - <expand macro="shell_command"/> + <command><![CDATA[ + + ############ first, create a directory to store all files + mkdir -p $report.files_path && + + + ############ save the tool installation directory to an environment variable + export TOOL_INSTALL_DIR='${__tool_directory__}' && + + + ######################### + ## + ## save user input option/argument pairs into a file + ## + ######################### + + ## first line will be the header + echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' && + + + + #################################################### + ## loop through repeats to get option/argument pairs + #################################################### + + + ############ option_argument_path_relative_to_a_tool + #for i in $option_argument_path_relative_to_a_tool_repeat: + #set $item = str($i.a_tool_output_dir) + "|" + str($i.value) + echo '$item' >> '$report.files_path/options_and_arguments.txt' && + #end for + + + ############ output_set + ## '$report' + ## '$report.files_path' + ####################### + export REPORT='$report' && + export TOOL_LOG='$tool_log' && + export REPORT_FILES_PATH='$report.files_path' && + + + ############ run render R script to render R markdowns + Rscript '${__tool_directory__}/list_paired_render.R' + + ]]></command> <inputs> - <expand macro="option_argument_path_relative_to_a_tool"/> + <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="0" default="0"> + <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/> + <param type="text" name="value" optional="true" label="relative path"/> + </repeat> </inputs> <outputs> <data format="html" name="report" label="${tool.name} report"/> <data format="txt" name="tool_log" label="${tool.name} log"/> - <collection type="list:paired" name="list_collection"> - <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" - directory="list_paired"/> + <collection type="list:paired" name="list_paired_collection"> + <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" directory="list_paired"/> </collection> </outputs> <citations>
--- a/elastic_expose_to_paired_collection.xml Mon Mar 26 18:40:39 2018 -0400 +++ b/elastic_expose_to_paired_collection.xml Sat Mar 31 21:32:17 2018 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="elastic_expose_list_paired_collection" name="elastic_expose_list_paired_collection" version="1.0.0"> +<tool id="elastic_expose_list_paired_collection" name="expose data (paired)" version="1.0.0"> <macros> <import>elastic_tool_wrappers_macros.xml</import> </macros> @@ -8,15 +8,63 @@ <expand macro="rmarkdown_requirements"/> </requirements> <expand macro="stdio"/> - <expand macro="shell_command"/> + <command><![CDATA[ + + ############ first, create a directory to store all files + mkdir -p $report.files_path && + + + ############ save the tool installation directory to an environment variable + export TOOL_INSTALL_DIR='${__tool_directory__}' && + + + ######################### + ## + ## save user input option/argument pairs into a file + ## + ######################### + + ## first line will be the header + echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' && + + + + #################################################### + ## loop through repeats to get option/argument pairs + #################################################### + + + ############ option_argument_path_relative_to_a_tool + #for i in $option_argument_path_relative_to_a_tool_repeat: + #set $item = str($i.a_tool_output_dir) + "|" + str($i.value) + echo '$item' >> '$report.files_path/options_and_arguments.txt' && + #end for + + + ############ output_set + ## '$report' + ## '$report.files_path' + ####################### + export REPORT='$report' && + export TOOL_LOG='$tool_log' && + export REPORT_FILES_PATH='$report.files_path' && + + + ############ run render R script to render R markdowns + Rscript '${__tool_directory__}/paired_render.R' + + ]]></command> <inputs> - <expand macro="option_argument_path_relative_to_a_tool"/> + <repeat name="option_argument_path_relative_to_a_tool_repeat" title="INPUT DATA PATH: relative to a tool output directory" min="2" default="2" max="2"> + <param name="a_tool_output_dir" type="data" optional="false" multiple="false" label="a tool output directory"/> + <param type="text" name="value" optional="true" label="relative path"/> + </repeat> </inputs> <outputs> <data format="html" name="report" label="${tool.name} report"/> <data format="txt" name="tool_log" label="${tool.name} log"/> - <collection type="paired" name="list_collection"> - <discover_datasets pattern="__name_and_ext__" directory="paired_dir" /> + <collection type="paired" name="paired_collection"> + <discover_datasets pattern="__name_and_ext__" directory="paired" /> </collection> </outputs> <citations>
--- a/elastic_tool_wrappers_macros.xml Mon Mar 26 18:40:39 2018 -0400 +++ b/elastic_tool_wrappers_macros.xml Sat Mar 31 21:32:17 2018 -0400 @@ -20,55 +20,6 @@ </xml> <!--shell command fragment--> - <xml name="shell_command"> - <command><![CDATA[ - echo $tool_name && - - ############ first, create a directory to store all files - mkdir -p $report.files_path && - - - ############ save the tool installation directory to an environment variable - export TOOL_INSTALL_DIR='${__tool_directory__}' && - - - ######################### - ## - ## save user input option/argument pairs into a file - ## - ######################### - - ## first line will be the header - echo 'tool_output_dir|relative_path' > '$report.files_path/options_and_arguments.txt' && - - - - #################################################### - ## loop through repeats to get option/argument pairs - #################################################### - - - ############ option_argument_path_relative_to_a_tool - #for i in $option_argument_path_relative_to_a_tool_repeat: - #set $item = str($i.a_tool_output_dir) + "|" + str($i.value) - echo '$item' >> '$report.files_path/options_and_arguments.txt' && - #end for - - - ############ output_set - ## '$report' - ## '$report.files_path' - ####################### - export REPORT='$report' && - export TOOL_LOG='$tool_log' && - export REPORT_FILES_PATH='$report.files_path' && - - - ############ run render R script to render R markdowns - Rscript '${__tool_directory__}/elastic_tool_render.R' - - ]]></command> - </xml> <!--<xml name="output_set">--> <!--<data format="html" name="report" label="${tool.name} report"/>-->
--- a/list.Rmd Mon Mar 26 18:40:39 2018 -0400 +++ b/list.Rmd Sat Mar 31 21:32:17 2018 -0400 @@ -1,5 +1,5 @@ --- -title: 'Dynamic tool' +title: 'Expose data (list)' output: html_document --- @@ -29,7 +29,7 @@ knitr::kable(df) ``` -```{r} +```{r, echo=FALSE} write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) if (nrow(df) > 0) { for (i in 1:nrow(df)) {
--- a/list_paired.Rmd Mon Mar 26 18:40:39 2018 -0400 +++ b/list_paired.Rmd Sat Mar 31 21:32:17 2018 -0400 @@ -1,5 +1,5 @@ --- -title: 'Dynamic tool' +title: 'Expose data (list:paired)' output: html_document --- @@ -29,7 +29,7 @@ knitr::kable(df) ``` -```{r} +```{r, echo=FALSE} write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) if (nrow(df) > 0) { for (i in 1:nrow(df)) {
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/list_paired_render.R Sat Mar 31 21:32:17 2018 -0400 @@ -0,0 +1,44 @@ +##============ Sink warnings and errors to a file ============== +## use the sink() function to wrap all code within it. +##============================================================== +zz = file(Sys.getenv('TOOL_LOG')) +sink(zz) +sink(zz, type = 'message') + +#------------import libraries-------------------- +options(stringsAsFactors = FALSE) + +library(rmarkdown) +library(stringr) +#------------------------------------------------ + +#------------------------------------------------ +options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), + sep = '|', header = TRUE) + +#------------------------------------------------ +# create three folders within working directory +dir.create('list_paired') + +#-----------------render Rmd-------------- +# copy R markdown file to working directory and render it within the working directory. +render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/list_paired.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 +# in the render function can cause empty report file when the tool runs in batch mode. +# the solution is to render the rmarkdown to a explicitly specified file and then copy the +# file to ${REPORT} +system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}') +system(command = 'sh ${REPORT_FILES_PATH}/script.sh') + +# rename files so that all files have the name pattern BASENAME_forward.EXT and BASENAME_reverse.EXT +from_files = list.files('list_paired', full.names = TRUE) +to_files = str_replace_all(from_files, c('_1', '_2'), c('_forward', '_reverse')) +file.rename(from = from_files, to = to_files) +#------------------------------------------ + + +##--------end of code rendering .Rmd templates---------------- +sink() +##=========== End of sinking output============================= \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/list_render.R Sat Mar 31 21:32:17 2018 -0400 @@ -0,0 +1,38 @@ +##============ Sink warnings and errors to a file ============== +## use the sink() function to wrap all code within it. +##============================================================== +zz = file(Sys.getenv('TOOL_LOG')) +sink(zz) +sink(zz, type = 'message') + +#------------import libraries-------------------- +options(stringsAsFactors = FALSE) + +library(rmarkdown) +#------------------------------------------------ + +#------------------------------------------------ +options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), + sep = '|', header = TRUE) + +#------------------------------------------------ +# create three folders within working directory +dir.create('list') + +#-----------------render Rmd-------------- +# copy R markdown file to working directory and render it within the working directory. +render(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/list.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 +# in the render function can cause empty report file when the tool runs in batch mode. +# the solution is to render the rmarkdown to a explicitly specified file and then copy the +# file to ${REPORT} +system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}') +system(command = 'sh ${REPORT_FILES_PATH}/script.sh') +#------------------------------------------ + + +##--------end of code rendering .Rmd templates---------------- +sink() +##=========== End of sinking output============================= \ No newline at end of file
--- a/paired.Rmd Mon Mar 26 18:40:39 2018 -0400 +++ b/paired.Rmd Sat Mar 31 21:32:17 2018 -0400 @@ -1,5 +1,5 @@ --- -title: 'Dynamic tool' +title: 'Expose data (paired)' output: html_document --- @@ -29,7 +29,7 @@ knitr::kable(df) ``` -```{r} +```{r, echo=FALSE} write('', file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/script.sh')) if (nrow(df) > 0) { for (i in 1:nrow(df)) {
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/paired_render.R Sat Mar 31 21:32:17 2018 -0400 @@ -0,0 +1,38 @@ +##============ Sink warnings and errors to a file ============== +## use the sink() function to wrap all code within it. +##============================================================== +zz = file(Sys.getenv('TOOL_LOG')) +sink(zz) +sink(zz, type = 'message') + +#------------import libraries-------------------- +options(stringsAsFactors = FALSE) + +library(rmarkdown) +#------------------------------------------------ + +#------------------------------------------------ +options_and_arguments = read.table(paste0(Sys.getenv('REPORT_FILES_PATH'), '/options_and_arguments.txt'), + sep = '|', header = TRUE) + +#------------------------------------------------ +# create three folders within working directory +dir.create('paired') + +#-----------------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'), + 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 +# in the render function can cause empty report file when the tool runs in batch mode. +# the solution is to render the rmarkdown to a explicitly specified file and then copy the +# file to ${REPORT} +system(command = 'cp ${REPORT_FILES_PATH}/report.html ${REPORT}') +system(command = 'sh ${REPORT_FILES_PATH}/script.sh') +#------------------------------------------ + + +##--------end of code rendering .Rmd templates---------------- +sink() +##=========== End of sinking output============================= \ No newline at end of file