aurora_htseq: rmarkdown_report

annotate rmarkdown_report_render.R @ 2:e08dd15646c6 draft

planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty

author	mingchen0919
date	Thu, 13 Dec 2018 23:45:31 -0500
parents	803f4888f36a
children

rev	line source
0 803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	1 ##============ Sink warnings and errors to a file ==============
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	2 ## use the sink() function to wrap all code within it.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	3 ##==============================================================
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	4 zz = file(paste0(Sys.getenv('REPORT_FILES_PATH'), '/.r_rendering.log.txt'))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	5 sink(zz)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	6 sink(zz, type = 'message')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	7
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	8 #============== preparation ====================================
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	9 # import libraries
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	10 #------------------------------------------------------------------
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	11 # ADD MORE LIBRARIES HERE IF YOUR TOOL DEPENDS ON OTHER R LIBRARIES
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	12 #------------------------------------------------------------------
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	13 library('getopt')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	14 library('rmarkdown')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	15 library('htmltools')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	16 library(knitr)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	17 #------------------------------------------------------------------
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	18 options(stringsAsFactors = FALSE)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	19
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	20
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	21 # define two helper functions
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	22 #-----: helper function 1
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	23 #' \code{getopt_specification_matrix} returns a getopt specification matrix.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	24 #'
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	25 #' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	26 #' The first column are short flags, the second column are argument masks, the third column
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	27 #' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	28 #' @param gtg_name the name of a running GTG.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	29 getopt_specification_matrix = function(specification_file,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	30 gtg_name = 'gtg',
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	31 tool_dir = Sys.getenv('TOOL_INSTALL_DIR')) {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	32 df = read.csv(
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	33 paste0(tool_dir, '/', specification_file),
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	34 header = TRUE,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	35 stringsAsFactors = FALSE
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	36 )
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	37 # check if there are duplicated short flags
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	38 short_flags = df[, 1]
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	39 if (length(unique(short_flags)) < length(short_flags)) {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	40 cat('----Duplicated short flags found ----\n')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	41 cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	42 stop('Duplicated short flags are not allowed.')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	43 }
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	44
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	45 # use short flags to generate long flags
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	46 long_flags = paste0('X_', df[, 1])
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	47
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	48 # specification matrix
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	49 df2 = data.frame(
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	50 long_flags = long_flags,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	51 short_flags = df[, 1],
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	52 argument_mask = df[, 2],
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	53 data_type = df[, 3]
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	54 )
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	55
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	56 as.matrix(df2)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	57 }
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	58
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	59 #-----: helper function 2
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	60 #' \code{file_tree} generate file tree of a directory in the format of HTML lists.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	61 #'
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	62 #' @param dir the path to the directory for generating the file tree.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	63 #' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	64 # define a recursive function to build html string of the file tree
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	65 file_tree = function(dir = '.') {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	66 # get the OUTPUT_DIR folder data: dataset_NUMBER_files
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	67 report_files_path = Sys.getenv('REPORT_FILES_PATH')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	68 output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	69
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	70 files = list.files(path = dir,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	71 recursive = FALSE,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	72 full.names = TRUE)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	73 # files also include directorys, need to remove directorys
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	74 files = files[!dir.exists(files)]
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	75 dirs = list.dirs(path = dir,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	76 recursive = FALSE,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	77 full.names = TRUE)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	78 tags$ul({
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	79 if (length(files) > 0) {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	80 lapply(files, function(x) {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	81 path_end = tail(strsplit(x, '/')[[1]], 1)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	82 href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	83 li_item = tags$li(tags$a(path_end, href = href_path))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	84 li_item$attribs = list('data-jstree' = '{"icon":"jstree-file"}')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	85 li_item
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	86 })
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	87 }
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	88 },
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	89 {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	90 if (length(dirs) > 0) {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	91 lapply(dirs, function(x) {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	92 path_end = tail(strsplit(x, '/')[[1]], 1)
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	93 # hide vakata-jstree-3.3.5 folder
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	94 if (!(path_end %in% c('vakata-jstree-3.3.5', 'rmarkdown_report_files', 'site_libs'))) {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	95 # x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	96 li_item = tags$li(path_end, file_tree(x))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	97 li_item$attribs = list('data-jstree' = '{"icon":"jstree-folder"}')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	98 li_item
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	99 }
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	100 })
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	101 }
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	102 })
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	103 }
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	104 #----------------- end of help functions -------------------------
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	105
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	106
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	107 # import getopt specification matrix from a csv file
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	108 opt = getopt(getopt_specification_matrix('command-line-arguments.csv',
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	109 tool_dir = Sys.getenv('TOOL_INSTALL_DIR')))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	110 # define environment variables for all input values. this is useful when we
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	111 # want to use input values by other programming language in r markdown
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	112 do.call(Sys.setenv, opt[-1])
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	113 #===============================================================
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	114
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	115
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	116 #======================== render Rmd files =========================
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	117 # copy jstree javascript library to tool output directory
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	118 file.copy(
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	119 from = paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/vakata-jstree-3.3.5'),
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	120 to = Sys.getenv('REPORT_FILES_PATH'),
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	121 recursive = TRUE
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	122 )
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	123
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	124 # if '_site.yml' file exists, this tool is assumed to render a website.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	125 # otherwise, it renders a single html.
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	126 if (file.exists(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/_site.yml'))) {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	127 # render a website
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	128 system(command = 'cp -r ${TOOL_INSTALL_DIR}/*.Rmd ${REPORT_FILES_PATH}')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	129 system(command = 'cp -r ${TOOL_INSTALL_DIR}/_site.yml ${REPORT_FILES_PATH}')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	130 render_site(input = Sys.getenv('REPORT_FILES_PATH'))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	131 } else {
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	132 # render a single html
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	133 system(command = 'cp -r ${TOOL_INSTALL_DIR}/rmarkdown_report.Rmd ${REPORT_FILES_PATH}')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	134 # add a few lines to 'rmarkdown_report.Rmd' to generate file tree outputs
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	135 jstree_lines = '
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	136 ## Outputs
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	137
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	138 ```{r, echo=FALSE}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	139 tags$div(id="jstree", file_tree(Sys.getenv(\'REPORT_FILES_PATH\')))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	140 ```'
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	141 write(
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	142 x = jstree_lines,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	143 append = TRUE,
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	144 file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	145 )
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	146 render(input = paste0(Sys.getenv('REPORT_FILES_PATH'), '/rmarkdown_report.Rmd'))
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	147 }
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	148 #===============================================================
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	149
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	150
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	151 #============== expose outputs to galaxy history ===============
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	152 system(command = 'sh ${TOOL_INSTALL_DIR}/expose-outputs-to-galaxy-history.sh')
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	153 #===============================================================
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	154
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	155
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	156 ##--------end of code rendering .Rmd templates----------------
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	157 sink()
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1 mingchen0919 parents: diff changeset	158 ##=========== End of sinking output=============================

Mercurial > repos > mingchen0919 > aurora_htseq

annotate rmarkdown_report_render.R @ 2:e08dd15646c6 draft