# HG changeset patch # User mingchen0919 # Date 1521495156 14400 # Node ID 7fd14296e7e09a55693f6eb0c1158b6bfaa32458 # Parent 4bc7752bfd7257d56493d3cc160c9c2dbc4730dc add es_gene_search diff -r 4bc7752bfd72 -r 7fd14296e7e0 es_gene_search.Rmd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/es_gene_search.Rmd Mon Mar 19 17:32:36 2018 -0400 @@ -0,0 +1,27 @@ +--- +title: 'HTML report title' +output: + html_document: + theme: cosmo + highlight: tango +--- + +```{r setup, include=FALSE, warning=FALSE, message=FALSE} +knitr::opts_chunk$set( + echo = TRUE, + error = TRUE +) +``` + + +# Code for computational analysis + +```{r 'step 1'} +opt +``` + +```{r 'ste[ 2'} + +``` + + diff -r 4bc7752bfd72 -r 7fd14296e7e0 es_gene_search.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/es_gene_search.csv Mon Mar 19 17:32:36 2018 -0400 @@ -0,0 +1,5 @@ +short flag,argument mask,data type,variable name,galaxy input type,description +o,1,character,report,data, +d,1,character,report.files_path,data, +O,1,character,organism,text, +R,1,character,fasta_results,text, diff -r 4bc7752bfd72 -r 7fd14296e7e0 es_gene_search.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/es_gene_search.sh Mon Mar 19 17:32:36 2018 -0400 @@ -0,0 +1,8 @@ +export TOOL_DIR='${__tool_directory__}' && + +Rscript '${__tool_directory__}/'es_gene_search_render.R + + -o '$report' + -d '$report.files_path' + -O '$organism' + -R '$fasta_results' diff -r 4bc7752bfd72 -r 7fd14296e7e0 es_gene_search.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/es_gene_search.xml Mon Mar 19 17:32:36 2018 -0400 @@ -0,0 +1,39 @@ + + gene search + + pandocr-getoptr-rmarkdownr-jsonliter-dtr-curl + + + + + + + + + + diff -r 4bc7752bfd72 -r 7fd14296e7e0 es_gene_search_render.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/es_gene_search_render.R Mon Mar 19 17:32:36 2018 -0400 @@ -0,0 +1,50 @@ +##============ Sink warnings and errors to a file ============== +## use the sink() function to wrap all code within it. +##============================================================== +zz = file('warnings_and_errors.txt') +sink(zz) +sink(zz, type = 'message') + +#------------import libraries-------------------- +options(stringsAsFactors = FALSE) + +library(getopt) +library(rmarkdown) +#------------------------------------------------ + + +#------------get arguments into R-------------------- +# load helper function +source(paste0(Sys.getenv('TOOL_DIR'), '/helper.R')) +# import getopt specification matrix from a csv file +opt = getopt(getopt_specification_matrix('/es_gene_search.csv')) +opt$X_t = Sys.getenv('TOOL_DIR') +#---------------------------------------------------- + + +#-----------using passed arguments in R +# to define system environment variables--- +do.call(Sys.setenv, opt[-1]) +#---------------------------------------------------- + +#---------- often used variables ---------------- +# OUTPUT_DIR: path to the output associated directory, which stores all outputs +# TOOL_DIR: path to the tool installation directory +OUTPUT_DIR = opt$X_d +TOOL_DIR = opt$X_t +OUTPUT_REPORT = opt$X_o +RMD_NAME = 'es_gene_search.Rmd' + +# create the output associated directory to store all outputs +dir.create(OUTPUT_DIR, recursive = TRUE) + +#-----------------render Rmd-------------- +render(paste0(TOOL_DIR, '/', RMD_NAME), output_file = OUTPUT_REPORT) +#------------------------------------------ + +#==============the end============== + + +##--------end of code rendering .Rmd templates---------------- +sink() +##=========== End of sinking output============================= diff -r 4bc7752bfd72 -r 7fd14296e7e0 get_content_types.xml --- a/get_content_types.xml Mon Mar 19 16:29:51 2018 -0400 +++ b/get_content_types.xml Mon Mar 19 17:32:36 2018 -0400 @@ -1,19 +1,11 @@ - - + + Tripal database explorer: get content types - - pandoc - r-getopt - r-rmarkdown - r-jsonlite - r-dt - r-curl - - - - - + pandocr-getoptr-rmarkdownr-jsonliter-dtr-curl + + + - - - - - - + + + + + - - + ]]> diff -r 4bc7752bfd72 -r 7fd14296e7e0 search_contents.xml --- a/search_contents.xml Mon Mar 19 16:29:51 2018 -0400 +++ b/search_contents.xml Mon Mar 19 17:32:36 2018 -0400 @@ -1,19 +1,12 @@ - - + + + some description - - pandoc - r-getopt - r-rmarkdown - r-jsonlite - r-dt - r-curl - - - - - + pandocr-getoptr-rmarkdownr-jsonliter-dtr-curl + + + - - -
- - - - - - - -
-
- - - -
- - - - - + +
+ + + - - + ]]>