# HG changeset patch
# User lgueguen
# Date 1538384876 14400
# Node ID de6d0b7c17afda1ef605530750dd6389a1848fe8
# Parent  d86ccac2a66049d6b63f8cf0f37c2a010b97b1df
release 1.6.3

diff -r d86ccac2a660 -r de6d0b7c17af README.md
--- a/README.md	Wed May 17 05:09:10 2017 -0400
+++ b/README.md	Mon Oct 01 05:07:56 2018 -0400
@@ -1,6 +1,6 @@
------------------------------------------------------------
-SARTools-Galaxy: a galaxy wrapper for SARTools version 1.3.2
------------------------------------------------------------
+--------------------------------------------------------------------------------------
+SARTools-Galaxy: a galaxy wrapper for SARTools (Statistical Analysis of RNA-Seq Tools) 
+--------------------------------------------------------------------------------------
 
 [![Build Status](https://travis-ci.org/PF2-pasteur-fr/SARTools-Galaxy.svg?branch=master)](https://travis-ci.org/PF2-pasteur-fr/SARTools-Galaxy)
 
@@ -12,10 +12,9 @@
 
 Requirements:
 -------------
-    R (3.3.0 or higher), Bio-conductor package 
-    SARTools package (1.3.2)
-    other R packages: DESeq2 (1.12.0 or higher), edgeR (3.12.0 or higher), genefilter, xtable and knitr
-    Rscript
+    These Galaxy tools need:
+    - R and the following R packages: SARTools, DESeq2, edgeR, genefilter, xtable and knitr.
+    - Rscript and optparse package
 
     SARTools can be downloaded on github (https://github.com/PF2-pasteur-fr/SARTools). More information about installation can be found at this url.
 
diff -r d86ccac2a660 -r de6d0b7c17af abims_sartools_deseq2.xml
--- a/abims_sartools_deseq2.xml	Wed May 17 05:09:10 2017 -0400
+++ b/abims_sartools_deseq2.xml	Mon Oct 01 05:07:56 2018 -0400
@@ -26,6 +26,7 @@
 	    --typeTrans $advanced_parameters.typeTrans
 	    --locfunc $advanced_parameters.locfunc
 	    --colors $advanced_parameters.colors
+            --forceCairoGraph $advanced_parameters.forceCairoGraph
     	#end if
 	## ouputs
 	@COMMAND_OUTPUTS@
@@ -45,23 +46,25 @@
             <when value="hide" />
             <when value="show">
 		<expand macro="batch_param" />
-                <param name="fitType" type="select" label="Mean-variance relationship" help="(-f, --fitType) Type of model for the mean-dispersion relationship. Parametric by default." >
+                <param type="select" label="Mean-variance relationship" argument="--fitType" help="Type of model for the mean-dispersion relationship. Parametric by default." >
           		<option value="parametric" selected="true">parametric</option>
 			<option value="local">local</option>
+			<option value="mean">mean</option>
 		</param>
-		<param name="cooksCutoff" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" help="(-o, --cooksCutoff) Checked by default."/>
-		<param name="independentFiltering" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" help="(-i, --independentFiltering) Checked by default."/>
+		<param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform the outliers detection" argument="--cooksCutoff" help="Checked by default."/>
+		<param type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Perform independent filtering" argument="--independentFiltering" help="Checked by default."/>
 		<expand macro="alpha_param" />
 		<expand macro="padjustmethod_param" />
-            	<param name="typeTrans" type="select" label="Transformation for PCA/clustering" help="(-T --typeTrans) Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." >
+            	<param type="select" label="Transformation for PCA/clustering" argument="--typeTrans" help="Method of transformation of the counts for the clustering and the PCA: 'VST' (default) for Variance Stabilizing Transformation, or 'rlog' for Regularized Log Transformation." >
                 	<option value="VST" selected="true">VST</option>
                 	<option value="rlog">rlog</option>
             	</param>
-            	<param name="locfunc" type="select" label="Estimation of the size factors" help="(-l --locfunc) 'median' (default) or 'shorth' from the genefilter package." >
+            	<param type="select" label="Estimation of the size factors" argument="--locfunc" help="'median' (default) or 'shorth' from the genefilter package." >
                 	<option value="median" selected="true">median</option>
                 	<option value="shorth">shorth</option>
             	</param>
 		<expand macro="colors_param" />
+		<expand macro="forceCairoGraph_param" />
             </when>
         </conditional>
 
@@ -85,7 +88,7 @@
             <output name="log">
                 <assert_contents>
                     <has_text text="KO vs WT    0.1       171" />
-                    <has_text text="KO vs WT    2584   2665 5249" />
+                    <has_text text="KO vs WT    2583   2663 5246" />
                     <has_text text="HTML report created" />
                 </assert_contents>
             </output>
@@ -142,6 +145,7 @@
 	* **typeTrans:** method of transformation of the counts for the clustering and the PCA (default is "VST" for Variance Stabilizing Transformation, or "rlog" for Regularized Log Transformation);
 	* **locfunc:** function used for the estimation of the size factors (default is "median", or "shorth" from the genefilter package);
 	* **colors:** colors used for the figures (one per biological condition), 8 are given by default.
+	* **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo").
 
 
 ------------
diff -r d86ccac2a660 -r de6d0b7c17af abims_sartools_deseq2_wrapper.py
--- a/abims_sartools_deseq2_wrapper.py	Wed May 17 05:09:10 2017 -0400
+++ b/abims_sartools_deseq2_wrapper.py	Mon Oct 01 05:07:56 2018 -0400
@@ -33,6 +33,7 @@
     parser.add_argument('--typeTrans')
     parser.add_argument('--locfunc')
     parser.add_argument('--colors')
+    parser.add_argument('--forceCairoGraph')
     parser.add_argument('--figures_html')
     parser.add_argument('--figures_html_files_path')
     parser.add_argument('--tables_html')
@@ -57,6 +58,7 @@
     typeTrans=args.typeTrans
     locfunc=args.locfunc
     colors=args.colors
+    forceCairoGraph=args.forceCairoGraph
     figures_html=args.figures_html
     figures_html_files_path=args.figures_html_files_path
     tables_html=args.tables_html
@@ -99,6 +101,8 @@
         cmd+="--locfunc %s " % (locfunc)
     if colors:
         cmd+="--colors %s " % (colors)
+    if forceCairoGraph:
+        cmd+="--forceCairoGraph %s " % (forceCairoGraph)
     cmd+="> %s 2>&1" % (log)
     print("Rscript command: %s") % (cmd)
     os.system(cmd)
diff -r d86ccac2a660 -r de6d0b7c17af abims_sartools_edger.xml
--- a/abims_sartools_edger.xml	Wed May 17 05:09:10 2017 -0400
+++ b/abims_sartools_edger.xml	Mon Oct 01 05:07:56 2018 -0400
@@ -25,6 +25,7 @@
 	    --geneSelection $advanced_parameters.geneSelection
 	    --normalizationMethod $advanced_parameters.normalizationMethod
 	    --colors $advanced_parameters.colors
+            --forceCairoGraph $advanced_parameters.forceCairoGraph
     	#end if
 	## ouputs
 	@COMMAND_OUTPUTS@
@@ -46,17 +47,18 @@
 		<expand macro="batch_param" />
 		<expand macro="alpha_param" />
 		<expand macro="padjustmethod_param" />
-		<param name="cpmCutoff" type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" help="(-m, --cpmCutoff) Set to 0 to disable filtering. Default is 1." />
-		<param name="geneSelection" type="select" label="Selection of the features in MDSPlot" help="(-g, --gene.selection) Default is 'pairwise'." >
+		<param type="integer" value="1" min="0" label="Counts-per-million cut-off to filter low counts" argument="--cpmCutoff" help="Set to 0 to disable filtering. Default is 1." />
+		<param name="geneSelection" type="select" label="Selection of the features in MDSPlot" argument="--gene.selection" help="Default is 'pairwise'." >
                 	<option value="pairwise" selected="true">pairwise</option>
                 	<option value="common">common</option>
 		</param>
-		<param name="normalizationMethod" type="select" label="Normalization method in calcNormFactors" help="(-n, --normalizationMethod) 'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." >
+		<param type="select" label="Normalization method in calcNormFactors" argument="--normalizationMethod" help="'TMM' (default), 'RLE' (DESeq method) or 'upperquartile'." >
                 	<option value="TMM" selected="true">TMM</option>
                 	<option value="RLE">RLE</option>
                 	<option value="upperquartile">upperquartile</option>
 		</param>
 		<expand macro="colors_param" />
+		<expand macro="forceCairoGraph_param" />
             </when>
         </conditional>
 
@@ -159,6 +161,7 @@
 	* **gene.selection:** method of selection of the features for the MultiDimensional Scaling plot ("pairwise" by default or common);
 	* **normalizationMethod:** normalization method in calcNormFactors(): "TMM" (default), "RLE" (DESeq method) or "upperquartile";
 	* **colors:** colors used for the figures (one per biological condition), 8 are given by default.
+	* **forceCairoGraph:** TRUE or FALSE (default) to force the use of cairo with options(bitmapType="cairo").
 
 
 ------------
diff -r d86ccac2a660 -r de6d0b7c17af abims_sartools_edger_wrapper.py
--- a/abims_sartools_edger_wrapper.py	Wed May 17 05:09:10 2017 -0400
+++ b/abims_sartools_edger_wrapper.py	Mon Oct 01 05:07:56 2018 -0400
@@ -31,6 +31,7 @@
     parser.add_argument('--geneSelection')
     parser.add_argument('--normalizationMethod')
     parser.add_argument('--colors')
+    parser.add_argument('--forceCairoGraph')
     parser.add_argument('--figures_html')
     parser.add_argument('--figures_html_files_path')
     parser.add_argument('--tables_html')
@@ -53,6 +54,7 @@
     geneSelection=args.geneSelection
     normalizationMethod=args.normalizationMethod
     colors=args.colors
+    forceCairoGraph=args.forceCairoGraph
     figures_html=args.figures_html
     figures_html_files_path=args.figures_html_files_path
     tables_html=args.tables_html
@@ -91,6 +93,8 @@
         cmd+="--normalizationMethod %s " % (normalizationMethod)
     if colors:
         cmd+="--colors %s " % (colors)
+    if forceCairoGraph:
+        cmd+="--forceCairoGraph %s " % (forceCairoGraph)
     cmd+="> %s 2>&1" % (log)
     print("Rscript command: %s") % (cmd)
     os.system(cmd)
diff -r d86ccac2a660 -r de6d0b7c17af macros.xml
--- a/macros.xml	Wed May 17 05:09:10 2017 -0400
+++ b/macros.xml	Mon Oct 01 05:07:56 2018 -0400
@@ -1,11 +1,11 @@
 <macros>
 
-    <token name="@WRAPPER_VERSION@">1.3.2</token>
+    <token name="@WRAPPER_VERSION@">1.6.3</token>
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="1.3.2">r-sartools</requirement>
-            <requirement type="package" version="1.3.2">r-optparse</requirement>
+            <requirement type="package" version="1.6.3">r-sartools</requirement>
+            <requirement type="package" version="1.6.0">r-optparse</requirement>
         </requirements>
     </xml>
     
@@ -52,28 +52,28 @@
   </token>
 
   <macro name="basic_parameters">
-        <param name="projectName" type="text" value="Project" label="Name of the project used for the report" help="(-P, --projectName) No space allowed." >
+        <param type="text" value="Project" label="Name of the project used for the report" argument="--projectName" help="No space allowed." >
 		<validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
 	</param>
-        <param name="author" type="text" value="Galaxy" label="Name of the report author" help="(-A, --author) No space allowed." >
+        <param type="text" value="Galaxy" label="Name of the report author" argument="--author" help="No space allowed." >
 		<validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
 	</param>
-        <param name="targetFile" type="data" format="txt" label="Design / target file" help="(-t, --targetFile) See the help section below for details on the required format." />        
-        <param name="rawDir" type="data" format="no_unzip.zip,zip" label="Zip file containing raw counts files" help="(-r, --rawDir) See the help section below for details on the required format." />        
-        <param name="featuresToRemove" type="text" size="100" value="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual" label="Names of the features to be removed" help="(-F, --featuresToRemove) Separate the features with a comma, no space allowed. More than once can be specified. Specific HTSeq-count information and rRNA for example. Default are 'alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual'." >
+        <param type="data" format="txt" label="Design / target file" argument="--targetFile" help="See the help section below for details on the required format." />        
+        <param type="data" format="no_unzip.zip,zip" label="Zip file containing raw counts files" argument="--rawDir" help="See the help section below for details on the required format." />        
+        <param type="text" size="100" value="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual" label="Names of the features to be removed" argument="--featuresToRemove" help="Separate the features with a comma, no space allowed. More than once can be specified. Specific HTSeq-count information and rRNA for example. Default are 'alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual'." >
 		<validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
 	</param>
-        <param name="varInt" type="text" value="group" label="Factor of interest" help="(-v, --varInt) Biological condition in the target file. Default is 'group'." >
+        <param type="text" value="group" label="Factor of interest" argument="--varInt" help="Biological condition in the target file. Default is 'group'." >
 		<validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
 	</param>
-        <param name="condRef" type="text" value="WT" label="Reference biological condition" help="(-c, --condRef) Reference biological condition used to compute fold-changes, must be one of the levels of 'Factor of interest'." >
+        <param type="text" value="WT" label="Reference biological condition" argument="--condRef" help="Reference biological condition used to compute fold-changes, must be one of the levels of 'Factor of interest'." >
 		<validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
 	</param>
   </macro>
 
   <macro name="batch_param">
 		<conditional name="batch_condition">
-			<param name="condition" type="boolean" checked="false" truevalue="batch" falsevalue="NULL" label="Add a blocking factor" help="(-b, --batch) Adjustment variable to use as a batch effect. Default: unchecked if no batch effect needs to be taken into account."/>
+			<param name="condition" type="boolean" checked="false" truevalue="batch" falsevalue="NULL" label="Add a blocking factor" argument="--batch" help="Adjustment variable to use as a batch effect. Default: unchecked if no batch effect needs to be taken into account."/>
             		<when value="NULL" />
 			<when value="batch">
 				<param name="batch" type="text" value="batch" label="Blocking factor value" help="Must be a column of the target file" >
@@ -84,11 +84,11 @@
   </macro>
 
   <macro name="alpha_param">
-		<param name="alpha" type="float" value="0.05" min="0" max="1" label="Threshold of statistical significance" help="(-a, --alpha) Significance threshold applied to the adjusted p-values to select the differentially expressed features. Default is 0.05. The comma is not allowed as decimal separator, use a point instead." />
+		<param type="float" value="0.05" min="0" max="1" label="Threshold of statistical significance" argument="--alpha" help="Significance threshold applied to the adjusted p-values to select the differentially expressed features. Default is 0.05. The comma is not allowed as decimal separator, use a point instead." />
   </macro>
 
   <macro name="padjustmethod_param">
-		<param name="pAdjustMethod" type="select" label="p-value adjustment method" help="(-p, --pAdjustMethod) p-value adjustment method for multiple testing. 'BH' by default, 'BY' or any value of p.adjust.methods." >
+		<param type="select" label="p-value adjustment method" argument="--pAdjustMethod" help="p-value adjustment method for multiple testing. 'BH' by default, 'BY' or any value of p.adjust.methods." >
                 	<option value="BH" selected="true">BH</option>
                 	<option value="BY">BY</option>
                 	<option value="bonferroni">bonferroni</option>
@@ -100,11 +100,15 @@
   </macro>
 
   <macro name="colors_param">
-		<param name="colors" type="text" size="100" value="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange" label="Colors of each biological condition on the plots: 'col1,col2,col3,col4'"           help="(-C, --colors) Separate the colors with a comma, no space allowed. Default are 'dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange'." >
+		<param type="text" size="100" value="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange" label="Colors of each biological condition on the plots: 'col1,col2,col3,col4'" argument="--colors" help="Separate the colors with a comma, no space allowed. Default are 'dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange'." >
 			<validator type="regex" message="Field requires a value. No space allowed.">\S+</validator>
 		</param>
   </macro>
 
+  <macro name="forceCairoGraph_param">
+		<param type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Activate cairo type" argument="--forceCairoGraph" help="Unchecked by default." />
+  </macro>
+
   <macro name="outputs">
         <data name="report_html" format="html"    label="${tool.name} report" /> 
         <data name="tables_html" format="html"    label="${tool.name} tables" /> 
diff -r d86ccac2a660 -r de6d0b7c17af pre_sartools.xml
--- a/pre_sartools.xml	Wed May 17 05:09:10 2017 -0400
+++ b/pre_sartools.xml	Mon Oct 01 05:07:56 2018 -0400
@@ -1,5 +1,8 @@
 <tool id="presartools" name="Preprocess files for SARTools" version="0.1.0">
     <description>generate design/target file and archive for SARTools inputs</description>
+    <stdio>
+        <regex match="WARNING:galaxy.model:Datatype class not found" level="warning"/>
+    </stdio>
     <command interpreter="python">
         pre_sartools.py
         --outfile=$outfile
diff -r d86ccac2a660 -r de6d0b7c17af template_script_DESeq2_CL.r
--- a/template_script_DESeq2_CL.r	Wed May 17 05:09:10 2017 -0400
+++ b/template_script_DESeq2_CL.r	Mon Oct 01 05:07:56 2018 -0400
@@ -1,192 +1,192 @@
-#!/local/gensoft2/exe/R/3.1.2/bin/Rscript
-
-# to run this script, use one of these commands:
-# Rscript --no-save --no-restore --verbose template_script_DESeq2_CL.r -r raw -v group -c T0 > log.txt 2>&1
-# Rscript template_script_DESeq2_CL.r -r raw -v group -c T0
-
-# to get help:
-# Rscript template_script_DESeq2_CL.r --help
-
-################################################################################
-### R script to compare several conditions with the SARTools and DESeq2 packages
-### Hugo Varet
-### April 20th, 2015
-### designed to be executed with SARTools 1.1.0
-################################################################################
-
-rm(list=ls())                                        # remove all the objects from the R session
-library(optparse)                                    # to run the script in command lines
-
-# options list with associated default value.
-option_list <- list( 
-make_option(c("-P", "--projectName"),
-			default=basename(getwd()),
-			dest="projectName",
-			help="name of the project used for the report [default: name of the current directory]."),
-
-make_option(c("-A", "--author"),
-			default=Sys.info()[7],
-			dest="author",
-			help="name of the report author [default: %default]."),
-
-make_option(c("-t", "--targetFile"),
-			default="target.txt",
-			dest="targetFile",
-			help="path to the design/target file [default: %default]."),
-
-make_option(c("-r", "--rawDir"),
-			default="raw",
-			dest="rawDir",
-			help="path to the directory containing the HTSeq files [default: %default]."),
-
-make_option(c("-F", "--featuresToRemove"),
-			default="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual",
-			dest="FTR",
-			help="names of the features to be removed, more than once can be specified [default: %default]"),
-			
-make_option(c("-v", "--varInt"),
-			default="group",
-			dest="varInt", 
-			help="factor of interest [default: %default]"),
-
-make_option(c("-c", "--condRef"),
-			default="WT",
-			dest="condRef",
-			help="reference biological condition [default: %default]"),
-
-make_option(c("-b", "--batch"),
-			default=NULL,
-			dest="batch",
-			help="blocking factor [default: %default] or \"batch\" for example"),
-
-make_option(c("-f", "--fitType"),
-			default="parametric",
-			dest="fitType", 
-			help="mean-variance relationship: [default: %default] or local"),
-
-make_option(c("-o", "--cooksCutoff"),
-			default=TRUE,
-			dest="cooksCutoff", 
-			help="perform the outliers detection (default is TRUE)"),
-
-make_option(c("-i", "--independentFiltering"),
-			default=TRUE,
-			dest="independentFiltering",
-			help="perform independent filtering (default is TRUE)"),
-
-make_option(c("-a", "--alpha"),
-			default=0.05,
-			dest="alpha", 
-			help="threshold of statistical significance [default: %default]"),
-
-make_option(c("-p", "--pAdjustMethod"),
-			default="BH",
-			dest="pAdjustMethod", 
-			help="p-value adjustment method: \"BH\" or \"BY\" [default: %default]"),
-
-make_option(c("-T", "--typeTrans"),
-			default="VST",
-			dest="typeTrans", 
-			help="transformation for PCA/clustering: \"VST\" ou \"rlog\" [default: %default]"),
-
-make_option(c("-l", "--locfunc"),
-			default="median",
-			dest="locfunc", 
-			help="median or shorth to estimate the size factors [default: %default]"),
-
-make_option(c("-C", "--colors"),
-			default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",
-			dest="cols",
-			help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]")
-)
-
-# now parse the command line to check which option is given and get associated values
-parser <- OptionParser(usage="usage: %prog [options]",
-					   option_list=option_list, 
-					   description="Compare two or more biological conditions in a RNA-Seq framework with DESeq2.",
-					   epilogue="For comments, bug reports etc... please contact Hugo Varet <hugo.varet@pasteur.fr>")
-opt <- parse_args(parser, args=commandArgs(trailingOnly=TRUE), positional_arguments=0)$options
-
-# get options and arguments
-workDir <- getwd()
-projectName <- opt$projectName                       # name of the project
-author <- opt$author	                             # author of the statistical analysis/report
-targetFile <- opt$targetFile                         # path to the design/target file
-rawDir <- opt$rawDir        						 # path to the directory containing raw counts files
-featuresToRemove <- unlist(strsplit(opt$FTR, ","))   # names of the features to be removed (specific HTSeq-count information and rRNA for example)
-varInt <- opt$varInt                                 # factor of interest
-condRef <- opt$condRef                               # reference biological condition
-batch <- opt$batch                                   # blocking factor: NULL (default) or "batch" for example
-fitType <- opt$fitType                               # mean-variance relationship: "parametric" (default) or "local"
-cooksCutoff <- opt$cooksCutoff                       # outliers detection threshold (NULL to let DESeq2 choosing it)
-independentFiltering <- opt$independentFiltering     # TRUE/FALSE to perform independent filtering (default is TRUE)
-alpha <- as.numeric(opt$alpha)                       # threshold of statistical significance
-pAdjustMethod <- opt$pAdjustMethod                   # p-value adjustment method: "BH" (default) or "BY"
-typeTrans <- opt$typeTrans                           # transformation for PCA/clustering: "VST" ou "rlog"
-locfunc <- opt$locfunc                               # "median" (default) or "shorth" to estimate the size factors
-colors <- unlist(strsplit(opt$cols, ","))            # vector of colors of each biologicial condition on the plots
-	
-# print(paste("workDir", workDir))
-# print(paste("projectName", projectName))
-# print(paste("author", author))
-# print(paste("targetFile", targetFile))
-# print(paste("rawDir", rawDir))
-# print(paste("varInt", varInt))
-# print(paste("condRef", condRef))
-# print(paste("batch", batch))
-# print(paste("fitType", fitType))
-# print(paste("cooksCutoff", cooksCutoff))
-# print(paste("independentFiltering", independentFiltering))
-# print(paste("alpha", alpha))
-# print(paste("pAdjustMethod", pAdjustMethod))
-# print(paste("typeTrans", typeTrans))
-# print(paste("locfunc", locfunc))
-# print(paste("featuresToRemove", featuresToRemove))
-# print(paste("colors", colors))
-
-################################################################################
-###                             running script                               ###
-################################################################################
-# setwd(workDir)
-library(SARTools)
-
-# checking parameters
-problem <- checkParameters.DESeq2(projectName=projectName,author=author,targetFile=targetFile,
-                       rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt,
-                       condRef=condRef,batch=batch,fitType=fitType,cooksCutoff=cooksCutoff,
-                       independentFiltering=independentFiltering,alpha=alpha,pAdjustMethod=pAdjustMethod,
-                       typeTrans=typeTrans,locfunc=locfunc,colors=colors)
-if (problem) quit(save="yes")
-					   
-# loading target file
-target <- loadTargetFile(targetFile=targetFile, varInt=varInt, condRef=condRef, batch=batch)
-
-# loading counts
-counts <- loadCountData(target=target, rawDir=rawDir, featuresToRemove=featuresToRemove)
-
-# description plots
-majSequences <- descriptionPlots(counts=counts, group=target[,varInt], col=colors)
-
-# analysis with DESeq2
-out.DESeq2 <- run.DESeq2(counts=counts, target=target, varInt=varInt, batch=batch,
-                         locfunc=locfunc, fitType=fitType, pAdjustMethod=pAdjustMethod,
-                         cooksCutoff=cooksCutoff, independentFiltering=independentFiltering, alpha=alpha)
-
-# PCA + clustering
-exploreCounts(object=out.DESeq2$dds, group=target[,varInt], typeTrans=typeTrans, col=colors)
-
-# summary of the analysis (boxplots, dispersions, diag size factors, export table, nDiffTotal, histograms, MA plot)
-summaryResults <- summarizeResults.DESeq2(out.DESeq2, group=target[,varInt], col=colors,
-                                          independentFiltering=independentFiltering, 
-                                          cooksCutoff=cooksCutoff, alpha=alpha)
-
-# save image of the R session
-save.image(file=paste0(projectName, ".RData"))
-
-# generating HTML report
-writeReport.DESeq2(target=target, counts=counts, out.DESeq2=out.DESeq2, summaryResults=summaryResults,
-                   majSequences=majSequences, workDir=workDir, projectName=projectName, author=author,
-                   targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt,
-                   condRef=condRef, batch=batch, fitType=fitType, cooksCutoff=cooksCutoff,
-                   independentFiltering=independentFiltering, alpha=alpha, pAdjustMethod=pAdjustMethod,
-                   typeTrans=typeTrans, locfunc=locfunc, colors=colors)
+################################################################################
+### R script to compare several conditions with the SARTools and DESeq2 packages
+### Hugo Varet
+### March 20th, 2018
+### designed to be executed with SARTools 1.6.3
+### run "Rscript template_script_DESeq2_CL.r --help" to get some help
+################################################################################
+
+rm(list=ls())                                        # remove all the objects from the R session
+library(optparse)                                    # to run the script in command lines
+
+# options list with associated default value.
+option_list <- list( 
+make_option(c("-P", "--projectName"),
+			default=basename(getwd()),
+			dest="projectName",
+			help="name of the project used for the report [default: name of the current directory]."),
+
+make_option(c("-A", "--author"),
+			default=Sys.info()[7],
+			dest="author",
+			help="name of the report author [default: %default]."),
+
+make_option(c("-t", "--targetFile"),
+			default="target.txt",
+			dest="targetFile",
+			help="path to the design/target file [default: %default]."),
+
+make_option(c("-r", "--rawDir"),
+			default="raw",
+			dest="rawDir",
+			help="path to the directory containing the HTSeq files [default: %default]."),
+
+make_option(c("-F", "--featuresToRemove"),
+			default="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual",
+			dest="FTR",
+			help="names of the features to be removed, more than once can be specified [default: %default]"),
+			
+make_option(c("-v", "--varInt"),
+			default="group",
+			dest="varInt", 
+			help="factor of interest [default: %default]"),
+
+make_option(c("-c", "--condRef"),
+			default="WT",
+			dest="condRef",
+			help="reference biological condition [default: %default]"),
+
+make_option(c("-b", "--batch"),
+			default=NULL,
+			dest="batch",
+			help="blocking factor [default: %default] or \"batch\" for example"),
+
+make_option(c("-f", "--fitType"),
+			default="parametric",
+			dest="fitType", 
+			help="mean-variance relationship: [default: %default], local or mean"),
+
+make_option(c("-o", "--cooksCutoff"),
+			default=TRUE,
+			dest="cooksCutoff", 
+			help="perform the outliers detection (default is TRUE)"),
+
+make_option(c("-i", "--independentFiltering"),
+			default=TRUE,
+			dest="independentFiltering",
+			help="perform independent filtering (default is TRUE)"),
+
+make_option(c("-a", "--alpha"),
+			default=0.05,
+			dest="alpha", 
+			help="threshold of statistical significance [default: %default]"),
+
+make_option(c("-p", "--pAdjustMethod"),
+			default="BH",
+			dest="pAdjustMethod", 
+			help="p-value adjustment method: \"BH\" or \"BY\" [default: %default]"),
+
+make_option(c("-T", "--typeTrans"),
+			default="VST",
+			dest="typeTrans", 
+			help="transformation for PCA/clustering: \"VST\" ou \"rlog\" [default: %default]"),
+
+make_option(c("-l", "--locfunc"),
+			default="median",
+			dest="locfunc", 
+			help="median or shorth to estimate the size factors [default: %default]"),
+
+make_option(c("-C", "--colors"),
+			default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",
+			dest="cols",
+			help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]"),
+
+make_option(c("-g", "--forceCairoGraph"),
+            action="store_true",
+            default=FALSE,
+            dest="forceCairoGraph",
+            help="activate cairo type")
+
+)
+
+# now parse the command line to check which option is given and get associated values
+parser <- OptionParser(usage="usage: %prog [options]",
+					   option_list=option_list, 
+					   description="Compare two or more biological conditions in a RNA-Seq framework with DESeq2.",
+					   epilogue="For comments, bug reports etc... please contact Hugo Varet <hugo.varet@pasteur.fr>")
+opt <- parse_args(parser, args=commandArgs(trailingOnly=TRUE), positional_arguments=0)$options
+
+# get options and arguments
+workDir <- getwd()
+projectName <- opt$projectName                       # name of the project
+author <- opt$author	                             # author of the statistical analysis/report
+targetFile <- opt$targetFile                         # path to the design/target file
+rawDir <- opt$rawDir        						 # path to the directory containing raw counts files
+featuresToRemove <- unlist(strsplit(opt$FTR, ","))   # names of the features to be removed (specific HTSeq-count information and rRNA for example)
+varInt <- opt$varInt                                 # factor of interest
+condRef <- opt$condRef                               # reference biological condition
+batch <- opt$batch                                   # blocking factor: NULL (default) or "batch" for example
+fitType <- opt$fitType                               # mean-variance relationship: "parametric" (default), "local" or "mean"
+cooksCutoff <- opt$cooksCutoff                       # outliers detection threshold (NULL to let DESeq2 choosing it)
+independentFiltering <- opt$independentFiltering     # TRUE/FALSE to perform independent filtering (default is TRUE)
+alpha <- as.numeric(opt$alpha)                       # threshold of statistical significance
+pAdjustMethod <- opt$pAdjustMethod                   # p-value adjustment method: "BH" (default) or "BY"
+typeTrans <- opt$typeTrans                           # transformation for PCA/clustering: "VST" ou "rlog"
+locfunc <- opt$locfunc                               # "median" (default) or "shorth" to estimate the size factors
+colors <- unlist(strsplit(opt$cols, ","))            # vector of colors of each biologicial condition on the plots
+forceCairoGraph <- opt$forceCairoGraph				 # force cairo as plotting device if enabled
+# print(paste("workDir", workDir))
+# print(paste("projectName", projectName))
+# print(paste("author", author))
+# print(paste("targetFile", targetFile))
+# print(paste("rawDir", rawDir))
+# print(paste("varInt", varInt))
+# print(paste("condRef", condRef))
+# print(paste("batch", batch))
+# print(paste("fitType", fitType))
+# print(paste("cooksCutoff", cooksCutoff))
+# print(paste("independentFiltering", independentFiltering))
+# print(paste("alpha", alpha))
+# print(paste("pAdjustMethod", pAdjustMethod))
+# print(paste("typeTrans", typeTrans))
+# print(paste("locfunc", locfunc))
+# print(paste("featuresToRemove", featuresToRemove))
+# print(paste("colors", colors))
+
+################################################################################
+###                             running script                               ###
+################################################################################
+# setwd(workDir)
+library(SARTools)
+if (forceCairoGraph) options(bitmapType="cairo")
+
+# checking parameters
+problem <- checkParameters.DESeq2(projectName=projectName,author=author,targetFile=targetFile,
+                       rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt,
+                       condRef=condRef,batch=batch,fitType=fitType,cooksCutoff=cooksCutoff,
+                       independentFiltering=independentFiltering,alpha=alpha,pAdjustMethod=pAdjustMethod,
+                       typeTrans=typeTrans,locfunc=locfunc,colors=colors)
+if (problem) quit(save="yes")
+					   
+# loading target file
+target <- loadTargetFile(targetFile=targetFile, varInt=varInt, condRef=condRef, batch=batch)
+
+# loading counts
+counts <- loadCountData(target=target, rawDir=rawDir, featuresToRemove=featuresToRemove)
+
+# description plots
+majSequences <- descriptionPlots(counts=counts, group=target[,varInt], col=colors)
+
+# analysis with DESeq2
+out.DESeq2 <- run.DESeq2(counts=counts, target=target, varInt=varInt, batch=batch,
+                         locfunc=locfunc, fitType=fitType, pAdjustMethod=pAdjustMethod,
+                         cooksCutoff=cooksCutoff, independentFiltering=independentFiltering, alpha=alpha)
+
+# PCA + clustering
+exploreCounts(object=out.DESeq2$dds, group=target[,varInt], typeTrans=typeTrans, col=colors)
+
+# summary of the analysis (boxplots, dispersions, diag size factors, export table, nDiffTotal, histograms, MA plot)
+summaryResults <- summarizeResults.DESeq2(out.DESeq2, group=target[,varInt], col=colors,
+                                          independentFiltering=independentFiltering, 
+                                          cooksCutoff=cooksCutoff, alpha=alpha)
+
+# save image of the R session
+save.image(file=paste0(projectName, ".RData"))
+
+# generating HTML report
+writeReport.DESeq2(target=target, counts=counts, out.DESeq2=out.DESeq2, summaryResults=summaryResults,
+                   majSequences=majSequences, workDir=workDir, projectName=projectName, author=author,
+                   targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt,
+                   condRef=condRef, batch=batch, fitType=fitType, cooksCutoff=cooksCutoff,
+                   independentFiltering=independentFiltering, alpha=alpha, pAdjustMethod=pAdjustMethod,
+                   typeTrans=typeTrans, locfunc=locfunc, colors=colors)
diff -r d86ccac2a660 -r de6d0b7c17af template_script_edgeR_CL.r
--- a/template_script_edgeR_CL.r	Wed May 17 05:09:10 2017 -0400
+++ b/template_script_edgeR_CL.r	Mon Oct 01 05:07:56 2018 -0400
@@ -1,175 +1,174 @@
-#!/local/gensoft2/exe/R/3.1.2/bin/Rscript
-
-# to run this script, use one of these commands:
-# Rscript --no-save --no-restore --verbose template_script_edgeR_CL.r -r raw -v group -c T0 > log.txt 2>&1
-# Rscript template_script_edgeR_CL.r -r raw -v group -c T0
-
-# to get help:
-# Rscript template_script_edgeR_CL.r --help
-
-################################################################################
-### R script to compare several conditions with the SARTools and edgeR packages
-### Hugo Varet
-### April 20th, 2015
-### designed to be executed with SARTools 1.1.0
-################################################################################
-
-rm(list=ls())                                        # remove all the objects from the R session
-library(optparse)                                    # to run the script in command lines
-
-# options list with associated default value.
-option_list <- list( 
-make_option(c("-P", "--projectName"),
-			default=basename(getwd()),
-			dest="projectName",
-			help="name of the project used for the report [default: name of the current directory]."),
-
-make_option(c("-A", "--author"),
-			default=Sys.info()[7],
-			dest="author",
-			help="name of the report author [default: %default]."),
-
-make_option(c("-t", "--targetFile"),
-			default="target.txt",
-			dest="targetFile",
-			help="path to the design/target file [default: %default]."),
-
-make_option(c("-r", "--rawDir"),
-			default="raw",
-			dest="rawDir",
-			help="path to the directory containing the HTSeq files [default: %default]."),		
-
-make_option(c("-F", "--featuresToRemove"),
-			default="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual",
-			dest="FTR",
-			help="names of the features to be removed, more than once can be specified [default: %default]"),
-			
-make_option(c("-v", "--varInt"),
-			default="group",
-			dest="varInt", 
-			help="factor of interest [default: %default]"),
-
-make_option(c("-c", "--condRef"),
-			default="WT",
-			dest="condRef",
-			help="reference biological condition [default: %default]"),
-
-make_option(c("-b", "--batch"),
-			default=NULL,
-			dest="batch",
-			help="blocking factor [default: %default] or \"batch\" for example"),
-
-make_option(c("-a", "--alpha"),
-			default=0.05,
-			dest="alpha", 
-			help="threshold of statistical significance [default: %default]"),
-
-make_option(c("-p", "--pAdjustMethod"),
-			default="BH",
-			dest="pAdjustMethod", 
-			help="p-value adjustment method: \"BH\" or \"BY\" [default: %default]"),
-
-make_option(c("-m", "--cpmCutoff"),
-			default=1,
-			dest="cpmCutoff", 
-			help="counts-per-million cut-off to filter low counts"),
-			
-make_option(c("-g", "--gene.selection"),
-			default="pairwise",
-			dest="gene.selection", 
-			help="selection of the features in MDSPlot [default: %default]"),
-			
-make_option(c("-n", "--normalizationMethod"),
-			default="TMM",
-			dest="normalizationMethod", 
-			help="normalization method in calcNormFactors: \"TMM\", \"RLE\" or \"upperquartile\" [default: %default]"),
-
-make_option(c("-C", "--colors"),
-			default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",
-			dest="cols",
-			help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]")
-)
-
-# now parse the command line to check which option is given and get associated values
-parser <- OptionParser(usage="usage: %prog [options]",
-					   option_list=option_list, 
-					   description="Compare two or more biological conditions in a RNA-Seq framework with edgeR.",
-					   epilogue="For comments, bug reports etc... please contact Hugo Varet <hugo.varet@pasteur.fr>")
-opt <- parse_args(parser, args=commandArgs(trailingOnly=TRUE), positional_arguments=0)$options
-
-# get options and arguments
-workDir <- getwd()
-projectName <- opt$projectName                       # name of the project
-author <- opt$author	                             # author of the statistical analysis/report
-targetFile <- opt$targetFile                         # path to the design/target file
-rawDir <- opt$rawDir								 # path to the directory containing raw counts files
-featuresToRemove <- unlist(strsplit(opt$FTR, ","))   # names of the features to be removed (specific HTSeq-count information and rRNA for example)
-varInt <- opt$varInt                                 # factor of interest
-condRef <- opt$condRef                               # reference biological condition
-batch <- opt$batch                                   # blocking factor: NULL (default) or "batch" for example
-alpha <- as.numeric(opt$alpha)                       # threshold of statistical significance
-pAdjustMethod <- opt$pAdjustMethod                   # p-value adjustment method: "BH" (default) or "BY"
-gene.selection <- opt$gene.selection                 # selection of the features in MDSPlot
-normalizationMethod <- opt$normalizationMethod       # normalization method in calcNormFactors
-cpmCutoff <- opt$cpmCutoff                           # counts-per-million cut-off to filter low counts
-colors <- unlist(strsplit(opt$cols, ","))            # vector of colors of each biologicial condition on the plots
-
-# print(paste("workDir", workDir))
-# print(paste("projectName", projectName))
-# print(paste("author", author))
-# print(paste("targetFile", targetFile))
-# print(paste("rawDir", rawDir))
-# print(paste("varInt", varInt))
-# print(paste("condRef", condRef))
-# print(paste("batch", batch))
-# print(paste("alpha", alpha))
-# print(paste("pAdjustMethod", pAdjustMethod))
-# print(paste("featuresToRemove", featuresToRemove))
-# print(paste("colors", colors))
-# print(paste("gene.selection", gene.selection))
-# print(paste("normalizationMethod", normalizationMethod))
-# print(paste("cpmCutoff", cpmCutoff))
-
-################################################################################
-###                             running script                               ###
-################################################################################
-# setwd(workDir)
-library(SARTools)
-
-# checking parameters
-problem <- checkParameters.edgeR(projectName=projectName,author=author,targetFile=targetFile,
-                      rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt,
-                      condRef=condRef,batch=batch,alpha=alpha,pAdjustMethod=pAdjustMethod,
-                      cpmCutoff=cpmCutoff,gene.selection=gene.selection,
-                      normalizationMethod=normalizationMethod,colors=colors)
-if (problem) quit(save="yes")
-					  
-# loading target file
-target <- loadTargetFile(targetFile=targetFile, varInt=varInt, condRef=condRef, batch=batch)
-
-# loading counts
-counts <- loadCountData(target=target, rawDir=rawDir, featuresToRemove=featuresToRemove)
-
-# description plots
-majSequences <- descriptionPlots(counts=counts, group=target[,varInt], col=colors)
-
-# edgeR analysis
-out.edgeR <- run.edgeR(counts=counts, target=target, varInt=varInt, condRef=condRef,
-                       batch=batch, cpmCutoff=cpmCutoff, normalizationMethod=normalizationMethod,
-                       pAdjustMethod=pAdjustMethod)
-
-# MDS + clustering
-exploreCounts(object=out.edgeR$dge, group=target[,varInt], gene.selection=gene.selection, col=colors)
-
-# summary of the analysis (boxplots, dispersions, export table, nDiffTotal, histograms, MA plot)
-summaryResults <- summarizeResults.edgeR(out.edgeR, group=target[,varInt], counts=counts, alpha=alpha, col=colors)
-
-# save image of the R session
-save.image(file=paste0(projectName, ".RData"))
-
-# generating HTML report
-writeReport.edgeR(target=target, counts=counts, out.edgeR=out.edgeR, summaryResults=summaryResults,
-                  majSequences=majSequences, workDir=workDir, projectName=projectName, author=author,
-                  targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt,
-                  condRef=condRef, batch=batch, alpha=alpha, pAdjustMethod=pAdjustMethod, colors=colors,
-                  gene.selection=gene.selection, normalizationMethod=normalizationMethod)
+################################################################################
+### R script to compare several conditions with the SARTools and edgeR packages
+### Hugo Varet
+### May 16th, 2018
+### designed to be executed with SARTools 1.6.3
+### run "Rscript template_script_edgeR_CL.r --help" to get some help
+################################################################################
+
+rm(list=ls())                                        # remove all the objects from the R session
+library(optparse)                                    # to run the script in command lines
+
+# options list with associated default value.
+option_list <- list( 
+make_option(c("-P", "--projectName"),
+			default=basename(getwd()),
+			dest="projectName",
+			help="name of the project used for the report [default: name of the current directory]."),
+
+make_option(c("-A", "--author"),
+			default=Sys.info()[7],
+			dest="author",
+			help="name of the report author [default: %default]."),
+
+make_option(c("-t", "--targetFile"),
+			default="target.txt",
+			dest="targetFile",
+			help="path to the design/target file [default: %default]."),
+
+make_option(c("-r", "--rawDir"),
+			default="raw",
+			dest="rawDir",
+			help="path to the directory containing the HTSeq files [default: %default]."),		
+
+make_option(c("-F", "--featuresToRemove"),
+			default="alignment_not_unique,ambiguous,no_feature,not_aligned,too_low_aQual",
+			dest="FTR",
+			help="names of the features to be removed, more than once can be specified [default: %default]"),
+			
+make_option(c("-v", "--varInt"),
+			default="group",
+			dest="varInt", 
+			help="factor of interest [default: %default]"),
+
+make_option(c("-c", "--condRef"),
+			default="WT",
+			dest="condRef",
+			help="reference biological condition [default: %default]"),
+
+make_option(c("-b", "--batch"),
+			default=NULL,
+			dest="batch",
+			help="blocking factor [default: %default] or \"batch\" for example"),
+
+make_option(c("-a", "--alpha"),
+			default=0.05,
+			dest="alpha", 
+			help="threshold of statistical significance [default: %default]"),
+
+make_option(c("-p", "--pAdjustMethod"),
+			default="BH",
+			dest="pAdjustMethod", 
+			help="p-value adjustment method: \"BH\" or \"BY\" [default: %default]"),
+
+make_option(c("-m", "--cpmCutoff"),
+			default=1,
+			dest="cpmCutoff", 
+			help="counts-per-million cut-off to filter low counts"),
+			
+make_option(c("-g", "--gene.selection"),
+			default="pairwise",
+			dest="gene.selection", 
+			help="selection of the features in MDSPlot [default: %default]"),
+			
+make_option(c("-n", "--normalizationMethod"),
+			default="TMM",
+			dest="normalizationMethod", 
+			help="normalization method in calcNormFactors: \"TMM\", \"RLE\" or \"upperquartile\" [default: %default]"),
+
+make_option(c("-C", "--colors"),
+			default="dodgerblue,firebrick1,MediumVioletRed,SpringGreen,chartreuse,cyan,darkorchid,darkorange",
+			dest="cols",
+			help="colors of each biological condition on the plots\n\t\t\"col1,col2,col3,col4\"\n\t\t[default: %default]"),
+
+make_option(c("-f", "--forceCairoGraph"),
+            action="store_true",
+            default=FALSE,
+            dest="forceCairoGraph",
+            help="activate cairo type")
+)
+
+# now parse the command line to check which option is given and get associated values
+parser <- OptionParser(usage="usage: %prog [options]",
+					   option_list=option_list, 
+					   description="Compare two or more biological conditions in a RNA-Seq framework with edgeR.",
+					   epilogue="For comments, bug reports etc... please contact Hugo Varet <hugo.varet@pasteur.fr>")
+opt <- parse_args(parser, args=commandArgs(trailingOnly=TRUE), positional_arguments=0)$options
+
+# get options and arguments
+workDir <- getwd()
+projectName <- opt$projectName                       # name of the project
+author <- opt$author	                             # author of the statistical analysis/report
+targetFile <- opt$targetFile                         # path to the design/target file
+rawDir <- opt$rawDir								 # path to the directory containing raw counts files
+featuresToRemove <- unlist(strsplit(opt$FTR, ","))   # names of the features to be removed (specific HTSeq-count information and rRNA for example)
+varInt <- opt$varInt                                 # factor of interest
+condRef <- opt$condRef                               # reference biological condition
+batch <- opt$batch                                   # blocking factor: NULL (default) or "batch" for example
+alpha <- as.numeric(opt$alpha)                       # threshold of statistical significance
+pAdjustMethod <- opt$pAdjustMethod                   # p-value adjustment method: "BH" (default) or "BY"
+gene.selection <- opt$gene.selection                 # selection of the features in MDSPlot
+normalizationMethod <- opt$normalizationMethod       # normalization method in calcNormFactors
+cpmCutoff <- opt$cpmCutoff                           # counts-per-million cut-off to filter low counts
+colors <- unlist(strsplit(opt$cols, ","))            # vector of colors of each biologicial condition on the plots
+forceCairoGraph <- opt$forceCairoGraph				 # force cairo as plotting device if enabled
+# print(paste("workDir", workDir))
+# print(paste("projectName", projectName))
+# print(paste("author", author))
+# print(paste("targetFile", targetFile))
+# print(paste("rawDir", rawDir))
+# print(paste("varInt", varInt))
+# print(paste("condRef", condRef))
+# print(paste("batch", batch))
+# print(paste("alpha", alpha))
+# print(paste("pAdjustMethod", pAdjustMethod))
+# print(paste("featuresToRemove", featuresToRemove))
+# print(paste("colors", colors))
+# print(paste("gene.selection", gene.selection))
+# print(paste("normalizationMethod", normalizationMethod))
+# print(paste("cpmCutoff", cpmCutoff))
+
+################################################################################
+###                             running script                               ###
+################################################################################
+# setwd(workDir)
+library(SARTools)
+if (forceCairoGraph) options(bitmapType="cairo")
+
+# checking parameters
+problem <- checkParameters.edgeR(projectName=projectName,author=author,targetFile=targetFile,
+                      rawDir=rawDir,featuresToRemove=featuresToRemove,varInt=varInt,
+                      condRef=condRef,batch=batch,alpha=alpha,pAdjustMethod=pAdjustMethod,
+                      cpmCutoff=cpmCutoff,gene.selection=gene.selection,
+                      normalizationMethod=normalizationMethod,colors=colors)
+if (problem) quit(save="yes")
+					  
+# loading target file
+target <- loadTargetFile(targetFile=targetFile, varInt=varInt, condRef=condRef, batch=batch)
+
+# loading counts
+counts <- loadCountData(target=target, rawDir=rawDir, featuresToRemove=featuresToRemove)
+
+# description plots
+majSequences <- descriptionPlots(counts=counts, group=target[,varInt], col=colors)
+
+# edgeR analysis
+out.edgeR <- run.edgeR(counts=counts, target=target, varInt=varInt, condRef=condRef,
+                       batch=batch, cpmCutoff=cpmCutoff, normalizationMethod=normalizationMethod,
+                       pAdjustMethod=pAdjustMethod)
+
+# MDS + clustering
+exploreCounts(object=out.edgeR$dge, group=target[,varInt], gene.selection=gene.selection, col=colors)
+
+# summary of the analysis (boxplots, dispersions, export table, nDiffTotal, histograms, MA plot)
+summaryResults <- summarizeResults.edgeR(out.edgeR, group=target[,varInt], counts=counts, alpha=alpha, col=colors)
+
+# save image of the R session
+save.image(file=paste0(projectName, ".RData"))
+
+# generating HTML report
+writeReport.edgeR(target=target, counts=counts, out.edgeR=out.edgeR, summaryResults=summaryResults,
+                  majSequences=majSequences, workDir=workDir, projectName=projectName, author=author,
+                  targetFile=targetFile, rawDir=rawDir, featuresToRemove=featuresToRemove, varInt=varInt,
+                  condRef=condRef, batch=batch, alpha=alpha, pAdjustMethod=pAdjustMethod, cpmCutoff=cpmCutoff,
+                  colors=colors, gene.selection=gene.selection, normalizationMethod=normalizationMethod)