diff i_adhore_configure_render.R @ 0:9755ce6ac4d5 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/i_adhore_configure_render.R	Tue Aug 08 12:53:57 2017 -0400
@@ -0,0 +1,102 @@
+
+##======= 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$ECHO = c('echo', 'e', '1', 'character')
+spec_list$G_ANALYSIS_FILES = c('g_analysis_files', 'G', '1', 'character')
+spec_list$BLAST_TABLE = c('blast_table', 'b', '1', 'character')
+spec_list$GAP_SIZE = c('gap_size', 'g', '1', 'character')
+spec_list$CLUSTER_GAP = c('cluster_gap', 'c', '1', 'character')
+spec_list$Q_VALUE = c('q_value', 'q', '1', 'character')
+spec_list$PROB_CUTOFF = c('prob_cutoff', 'p', '1', 'character')
+spec_list$ANCHOR_POINTS = c('anchor_points', 'a', '1', 'character')
+spec_list$ALIGNMENT_METHOD = c('alignment_method', 'm', '1', 'character')
+spec_list$LEVEL2ONLY = c('level2only', 'l', '1', 'character')
+spec_list$TABLE_TYPE = c('table_type', 'T', '1', 'character')
+spec_list$MULTI_HYPOTHESIS_CORRECTION = c('multi_hypothesis_correction', 'h', '1', 'character')
+
+
+##--------2. output report and report site directory --------------
+spec_list$I_ADHORE_CONFIGURE_TXT = c('i_adhore_configure_txt', 'x', '1', 'character')
+spec_list$OUTPUT_HTML = c('i_adhore_configure_html', 'o', '1', 'character')
+spec_list$OUTPUT_DIR = c('i_adhore_configure_dir', 'd', '1', 'character')
+
+
+##--------3. Rmd templates sitting in the tool directory ----------
+spec_list$I_ADHORE_CONFIGURE_RMD = c('i_adhore_configure_rmd', '-t', '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(dplyr)
+
+
+#----- 1. create the report directory ------------------------
+system(paste0('mkdir -p ', opt$i_adhore_configure_dir))
+# set working directory to output files directory
+setwd(opt$i_adhore_configure_dir)
+
+
+#----- 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.
+
+
+#----- 01 i_adhore_configure.Rmd -----------------------
+readLines(opt$i_adhore_configure_rmd) %>%
+    (function(x) {
+        gsub('ECHO', opt$echo, x)
+    }) %>%
+    (function(x) {
+        gsub('I_ADHORE_CONFIGURE_TXT', opt$i_adhore_configure_txt, x)
+    }) %>%
+    (function(x) {
+        fileConn = file('i_adhore_configure.Rmd')
+        writeLines(x, con=fileConn)
+        close(fileConn)
+    })
+
+
+#------ 3. render all Rmd files --------
+render('i_adhore_configure.Rmd', output_file = opt$i_adhore_configure_html)