diff charts.r @ 0:a87a3773d8ed draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ commit 87080d49913cfd40a77eda7e5834ac9c4bc30b0b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/charts.r	Fri Mar 09 08:23:08 2018 -0500
@@ -0,0 +1,116 @@
+#!/usr/bin/Rscript
+
+# load getopt library
+library('getopt');
+
+# convert multi parameter string (i.e. key1: value, key2: value, ...) to object
+split <- function(argument){
+    # process parameter string
+    options <- list()
+    list <- gsub("\\s","", argument)
+    list <- strsplit(list, ",")
+    if (length(list) > 0) {
+        list <- list[[1]]
+        for (entry in list) {
+            pair <- strsplit(entry, ":")
+            if (length(pair) > 0) {
+                pair <- pair[[1]]
+                if (length(pair) == 2) {
+                    options[[pair[1]]] <- pair[2]
+                }
+            }
+        }
+    }
+    return(options)
+}
+
+# get options, using the spec as defined by the enclosed list.
+spec = matrix(c(
+    'workdir',  'w', 1, 'character', 'Work directory',
+    'module',   'm', 1, 'character', 'Module name',
+    'input',    'i', 1, 'character', 'Input tabular file',
+    'columns',  'c', 1, 'character', 'Columns string',
+    'settings', 's', 1, 'character', 'Settings string',
+    'output',   'o', 1, 'character', 'Output tabular file',
+    'help',     'h', 0, '',          'Help',
+    'verbose',  'v', 0, '',          'Verbose'
+), byrow=TRUE, ncol=5);
+opt = getopt(spec);
+
+# show help
+if ( !is.null(opt$help) ||
+    is.null(opt$module) ||
+    is.null(opt$input) ||
+    is.null(opt$columns) ||
+    is.null(opt$output)) {
+    cat(getopt(spec, usage=TRUE))
+    q(status=1);
+}
+
+# read columns/settings
+columns = split(opt$columns)
+settings = split(opt$settings)
+
+# read table
+table <- read.table(opt$input, comment.char='#', fill=TRUE)
+
+# identify module file
+module_file = paste(opt$workdir, opt$module, '.r', sep='')
+
+# source module
+source(module_file)
+
+# run module
+l = wrapper (table, columns, settings)
+
+# header
+header_title <- '# title - Chart Utilities (charts)'
+header_date <- paste('# date -', Sys.time(), sep=' ')
+header_module <- paste('# module -', opt$module, sep=' ')
+header_settings <- paste('# settings -', opt$settings, sep=' ')
+header_columns <- paste('# columns -', opt$columns, sep=' ')
+
+# check result
+if (length(l) > 0) {
+    # print details
+    if (!is.null(opt$verbose)) {
+        print ('Columns:')
+        print (columns)
+        print ('Settings:')
+        print (settings)
+        print ('Result:')
+        print (l)
+    }
+
+    # create output file
+    output <- file(opt$output, open='wt')
+    
+    # write header
+    writeLines('#', output)
+    writeLines(header_title, output)
+    writeLines(header_date, output)
+    writeLines(header_module, output)
+    writeLines(header_settings, output)
+    writeLines(header_columns, output)
+    writeLines('#', output)
+    
+    # pad columns
+    rows <- max(unlist(lapply(l, length)))
+    padded <- lapply(l, function(col) {
+        length(col) = rows;
+        col
+    })
+    
+    # write table
+    write.table(padded, file=output, row.names=FALSE, col.names = FALSE, quote=FALSE, sep='\t')
+    
+    # close file
+    close(output)
+} else {
+    # print details
+    print ('Columns:')
+    print (columns)
+    print ('Settings:')
+    print (settings)
+    print ('No output generated.')
+}
\ No newline at end of file