# HG changeset patch
# User mingchen0919
# Date 1524081578 14400
# Node ID 7c54fd452b8ef0f546cf210df9276f324a7d1a44
# Parent aacd5f53ac996e221e0ebfa17b14f208670a7de0
add kableExtra package
diff -r aacd5f53ac99 -r 7c54fd452b8e helper.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/helper.R Wed Apr 18 15:59:38 2018 -0400
@@ -0,0 +1,72 @@
+#' \code{getopt_specification_matrix} returns a getopt specification matrix.
+#'
+#' @param specification_file a cvs file within the \code{galaxy_tool_directory} which stores getopt specification matrix data.
+#' The first column are short flags, the second column are argument masks, the third column
+#' is data types. The fourth column are variable names used in the tool XML. These three columns are required.
+#' @param gtg_name the name of a running GTG.
+getopt_specification_matrix = function(specification_file, gtg_name = 'gtg', tool_dir = Sys.getenv('TOOL_DIR')) {
+ df = read.csv(paste0(tool_dir, '/', specification_file),
+ header = TRUE, stringsAsFactors = FALSE)
+ # check if there are duplicated short flags
+ short_flags = df[, 1]
+ if (length(unique(short_flags)) < length(short_flags)) {
+ cat('----Duplicated short flags found ----\n')
+ cat('short flags: ', df[, 1][duplicated(df[, 1])], '\n')
+ stop('Duplicated short flags are not allowed.')
+ }
+
+ # use short flags to generate long flags
+ long_flags = paste0('X_', df[, 1])
+
+ # specification matrix
+ df2 = data.frame(long_flags = long_flags,
+ short_flags = df[, 1],
+ argument_mask = df[, 2],
+ data_type = df[, 3])
+
+ as.matrix(df2)
+}
+
+
+
+#' \code{file_tree} generate file tree of a directory in the format of HTML lists.
+#'
+#' @param dir the path to the directory for generating the file tree.
+#' @param output_dir the REPORT_FILES_PATH folder name, which has the name style: dataset_NUMBER_files.
+# define a recursive function to build html string of the file tree
+file_tree = function(dir = '.'){
+ # get the OUTPUT_DIR folder data: dataset_NUMBER_files
+ report_files_path = Sys.getenv('REPORT_FILES_PATH')
+ output_dir = tail(strsplit(report_files_path, '/')[[1]], 1)
+
+ files = list.files(path = dir, recursive = FALSE, full.names = TRUE)
+ # files also include directorys, need to remove directorys
+ files = files[!dir.exists(files)]
+ dirs = list.dirs(path = dir, recursive = FALSE, full.names = TRUE)
+ # hide vakata-jstree-3.3.5 folder
+ #jstree_index = grep(pattern = 'vakata-jstree-3.3.5', x = dirs)
+ #dirs = dirs[-jstree_index]
+ tags$ul(
+ {
+ if (length(files) > 0) {
+ lapply(files, function(x){
+ path_end = tail(strsplit(x, '/')[[1]],1)
+ href_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+ li_item = tags$li(tags$a(path_end, href=href_path))
+ li_item$attribs = list('data-jstree'='{"icon":"jstree-file"}')
+ li_item
+ })
+ }
+ },
+ {
+ if (length(dirs) > 0) {
+ lapply(dirs, function(x){
+ x_path = strsplit(x, paste0(output_dir, '/'))[[1]][2]
+ li_item = tags$li(x_path, file_tree(x))
+ li_item$attribs = list('data-jstree'='{"icon":"jstree-folder"}')
+ li_item
+ })
+ }
+ }
+ )
+}
diff -r aacd5f53ac99 -r 7c54fd452b8e htseq_count.Rmd
--- a/htseq_count.Rmd Wed Apr 18 13:17:28 2018 -0400
+++ b/htseq_count.Rmd Wed Apr 18 15:59:38 2018 -0400
@@ -42,29 +42,31 @@
-----------------------------------------
-```{bash, echo=FALSE}
-sh ${TOOL_INSTALL_DIR}/run_htseq-count.sh
-```
-
## Job script
* htseq-count analysis: [htseq-count.sh](htseq-count.sh)
+```{bash, echo=FALSE}
+sh ${TOOL_INSTALL_DIR}/run_htseq-count.sh
+```
+
+
## Counts
-```{r}
+```{r, echo=TRUE}
count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
colnames(count_data) = rep(sample_names, length = ncol(count_data))
-DT::datatable(count_data, caption = "htseq counts for each sample")
+kable(head(count_data))
```
-```{r}
+```{r, echo=FALSE}
# save count data as an R object
save(count_data, file = paste0(opt$X_d, '/counts.RData'))
```
-```{bash}
+```{bash, echo=FALSE}
+# expose counts.RData to galaxy history
cp ${X_d}/counts.RData ${X_O}
```
diff -r aacd5f53ac99 -r 7c54fd452b8e htseq_count.xml
--- a/htseq_count.xml Wed Apr 18 13:17:28 2018 -0400
+++ b/htseq_count.xml Wed Apr 18 15:59:38 2018 -0400
@@ -5,7 +5,7 @@
r-getopt
r-rmarkdown
htseq
- r-dt
+ r-kableextra
$report.files_path/.r_rendering.log.txt &&
- echo echo 'R markdown rendering started.' &&
-
Rscript '${__tool_directory__}/htseq_count_render.R'
-o $report
@@ -45,9 +43,7 @@
-i $idattr
-m $mode
-c $count
- -O $count_rdata &&
-
- echo 'R markdown rendering finished.'
+ -O $count_rdata
]]>
diff -r aacd5f53ac99 -r 7c54fd452b8e htseq_count_render.R
--- a/htseq_count_render.R Wed Apr 18 13:17:28 2018 -0400
+++ b/htseq_count_render.R Wed Apr 18 15:59:38 2018 -0400
@@ -11,6 +11,8 @@
library(getopt)
library(rmarkdown)
library(htmltools)
+library(kableExtra)
+library(magrittr)
# load helper functions
source(paste0(Sys.getenv('TOOL_INSTALL_DIR'), '/helper.R'))
# import getopt specification matrix from a csv file
diff -r aacd5f53ac99 -r 7c54fd452b8e run_htseq-count.sh
--- a/run_htseq-count.sh Wed Apr 18 13:17:28 2018 -0400
+++ b/run_htseq-count.sh Wed Apr 18 15:59:38 2018 -0400
@@ -10,9 +10,11 @@
-a ${X_a} \\
-t ${X_T} \\
-i ${X_i} \\
- -m ${X_m} > counts.txt
+ -m ${X_m} > htseq-counts-raw.txt
- grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' counts.txt > ${X_c}
+ grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' htseq-counts-raw.txt > counts.txt
+
+ cp counts.txt ${X_c}
EOF
sh htseq-count.sh
\ No newline at end of file