diff mirdeep2_render.R @ 0:963905bcb754 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mirdeep2_render.R	Tue Aug 08 13:14:41 2017 -0400
@@ -0,0 +1,164 @@
+##======= Handle arguments from command line ========
+# setup R error handline to go to stderr
+options(show.error.messages=FALSE,
+error=function(){
+    cat(geterrmessage(), file=stderr())
+    quit("no", 1, F)
+})
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc = Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+# suppress warning
+options(warn = -1)
+
+options(stringsAsFactors=FALSE, useFancyQuotes=FALSE)
+args = commandArgs(trailingOnly=TRUE)
+
+suppressPackageStartupMessages({
+    library(getopt)
+    library(tools)
+})
+
+# column 1: the long flag name
+# column 2: the short flag alias. A SINGLE character string
+# column 3: argument mask
+#           0: no argument
+#           1: argument required
+#           2: argument is optional
+# column 4: date type to which the flag's argument shall be cast.
+#           possible values: logical, integer, double, complex, character.
+spec_list=list()
+
+##------- 1. input data ---------------------
+spec_list$ECHO = c('echo', 'e', '1', 'character')
+spec_list$COLLASPED_READS = c('collapsed_reads', 'a', '1', 'character')
+spec_list$REFERENCE_GENOME = c('reference_genome', 'b', '1', 'character')
+spec_list$READS_MAPPING = c('reads_mapping', 'c', '1', 'character')
+
+##--------2. output report and report site directory --------------
+spec_list$OUTPUT_HTML = c('mirdeep2_html', 'o', '1', 'character')
+spec_list$OUTPUT_DIR = c('mirdeep2_output_dir', 'd', '1', 'character')
+spec_list$CSV_RESULT = c('csv_result', 'r', '1', 'character')
+spec_list$HTML_RESULT = c('html_result', 't', '1', 'character')
+spec_list$REPORT_LOG = c('report_log', 'u', '1', 'character')
+
+##---------other parameters---------
+spec_list$SPECIES_MATURE_MIRNA = c('species_mature_mirna', 'f', '2', 'character')
+spec_list$SPECIES_RELATED_MATURE_MIRRNA = c('related_species_mature_mirna', 'g', '2', 'character')
+spec_list$PRECURSOR_SEQUENCES = c('precursor_sequences', 'h', '2', 'character')
+spec_list$MIN_READ_STACK_HEIGHT = c('min_read_stack_height', 'j', '2', 'character')
+spec_list$MIN_SCORE_CUTOFF = c('min_score_cutoff', 'k',  '2', 'character')
+spec_list$RANDFOLD_ANALYSIS = c('randfold_analysis', 'l', '2', 'character')
+spec_list$MAX_PRECURSOR_NUMBER = c('max_precursor_number', 'm', '2', 'character')
+spec_list$SPECIES = c('species', 'n', '2', 'character')
+spec_list$SWITCH = c('switch', 'q', '2', 'character')
+
+##--------3. Rmd templates sitting in the tool directory ----------
+
+## _site.yml and index.Rmd files
+spec_list$SITE_YML = c('site_yml', 's', 1, 'character')
+spec_list$INDEX_Rmd = c('index_rmd', 'i', 1, 'character')
+
+## other Rmd body template files
+spec_list$MIRDEEP2_RMD = c('mirdeep2_rmd', 'p', '1', 'character')
+
+
+
+##------------------------------------------------------------------
+
+spec = t(as.data.frame(spec_list))
+opt = getopt(spec)
+# arguments are accessed by long flag name (the first column in the spec matrix)
+#                        NOT by element name in the spec_list
+# example: opt$help, opt$expression_file
+##====== End of arguments handling ==========
+
+#------ Load libraries ---------
+library(rmarkdown)
+library(plyr)
+# library(stringr)
+library(dplyr)
+# library(highcharter)
+# library(DT)
+# library(reshape2)
+# library(plotly)
+# library(formattable)
+library(htmltools)
+
+
+#----- 1. create the report directory ------------------------
+paste0('mkdir -p ', opt$mirdeep2_output_dir) %>%
+system()
+
+#----- 2. generate Rmd files with Rmd templates --------------
+#   a. templates without placeholder variables:
+#         copy templates from tool directory to the working directory.
+#   b. templates with placeholder variables:
+#         substitute variables with user input values and place them in the working directory.
+
+
+#----- mirdeep2.Rmd -----------------------
+readLines(opt$mirdeep2_rmd) %>%
+  (function(x) {
+    gsub('ECHO', opt$echo, x)
+  }) %>%
+  (function(x) {
+    gsub('COLLAPSED_READS', opt$collapsed_reads, x)
+  }) %>%
+  (function(x) {
+    gsub('REFERENCE_GENOME', opt$reference_genome, x)
+  }) %>%
+  (function(x) {
+    gsub('READS_MAPPING', opt$reads_mapping, x)
+  }) %>%
+  (function(x) {
+    gsub('SPECIES_MATURE_MIRNA', opt$species_mature_mirna, x)
+  }) %>%
+  (function(x) {
+    gsub('SPECIES_RELATED_MATURE_MIRNA', opt$related_species_mature_mirna, x)
+  }) %>%
+  (function(x) {
+    gsub('PRECURSOR_SEQUENCES', opt$precursor_sequences, x)
+  }) %>%
+  (function(x) {
+    gsub('MIN_READ_STACK_HEIGHT', opt$min_read_stack_height, x)
+  }) %>%
+  (function(x) {
+    gsub('MIN_SCORE_CUTOFF', opt$min_score_cutoff, x)
+  }) %>%
+  (function(x) {
+    gsub('RANDFOLD_ANALYSIS', opt$randfold_analysis, x)
+  }) %>%
+  (function(x) {
+    gsub('MAX_PRECURSOR_NUMBER', opt$max_precursor_number, x)
+  }) %>%
+  (function(x) {
+    gsub('SPECIES', opt$species, x)
+  }) %>%
+  (function(x) {
+    gsub('SWITCH', opt$switch, x)
+  }) %>%
+  (function(x) {
+    gsub('OUTPUT_DIR', opt$mirdeep2_output_dir, x)
+  }) %>%
+  (function(x) {
+    fileConn = file('mirdeep2.Rmd')
+    writeLines(x, con=fileConn)
+    close(fileConn)
+  })
+
+
+#------ 3. render all Rmd files with render() --------
+render('mirdeep2.Rmd',output_file = opt$mirdeep2_html)
+
+
+#-------4. manipulate outputs -----------------------------
+#   a. copy non-site files
+file.copy('result.csv', opt$csv_result, recursive=TRUE)
+file.copy('result.html', opt$html_result, recursive=TRUE)
+file.copy('report.log', opt$report_log, recursive=TRUE)
+
+
+
+