# HG changeset patch
# User ethevenot
# Date 1477068982 14400
# Node ID 6d3b7b6573d832c2c671ff80c065ca431bedeb59
# Parent  b4f5b5bc01dd3dd23aa422f9eca1de0777ed5657
planemo upload for repository https://github.com/workflow4metabolomics/qualitymetrics.git commit 60328240b89497f9dc7633b10b2a550b10da00c7

diff -r b4f5b5bc01dd -r 6d3b7b6573d8 README.md
--- a/README.md	Sat Aug 06 12:01:17 2016 -0400
+++ b/README.md	Fri Oct 21 12:56:22 2016 -0400
@@ -7,8 +7,8 @@
 
 ### Description
 
-**Version:** 2.2.4  
-**Date:** 2016-08-04  
+**Version:** 2.2.6  
+**Date:** 2016-10-21  
 **Author:** Marion Landi (INRA, PFEM), Mélanie Pétéra (INRA, PFEM), and Etienne A. Thévenot (CEA, LIST)  
 **Email:** [melanie.petera(at)clermont.inra.fr](mailto:melanie.petera@clermont.inra.fr), [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)  
 **Citation:**  
@@ -52,6 +52,12 @@
 
 ### News
 
+##### CHANGES IN VERSION 2.2.6  
+
+MINOR MODIFICATION  
+
+ * Graphic (pool_CV inferior to 30% metric): pools with a NaN value are now counted as having a value superior to 30% (to avoid generating a final NA metric value)  
+
 ##### CHANGES IN VERSION 2.2.4  
 
 INTERNAL MODIFICATION    
diff -r b4f5b5bc01dd -r 6d3b7b6573d8 build.xml
--- a/build.xml	Sat Aug 06 12:01:17 2016 -0400
+++ b/build.xml	Fri Oct 21 12:56:22 2016 -0400
@@ -36,7 +36,7 @@
 			<arg value="--conda_prefix"/>
 			<arg value="${conda.dir}"/>
 			<arg value="--galaxy_branch"/>
-			<arg value="release_16.01"/>
+			<arg value="release_16.07"/>
 			<arg value="--conda_dependency_resolution"/>
 			<arg value="${tool.xml}"/>
 		</exec>
diff -r b4f5b5bc01dd -r 6d3b7b6573d8 qualitymetrics_config.xml
--- a/qualitymetrics_config.xml	Sat Aug 06 12:01:17 2016 -0400
+++ b/qualitymetrics_config.xml	Fri Oct 21 12:56:22 2016 -0400
@@ -1,10 +1,10 @@
-<tool id="quality_metrics" name="Quality Metrics" version="2.2.4">
+<tool id="quality_metrics" name="Quality Metrics" version="2.2.6">
   <description>Metrics and graphics to check the quality of the data</description>
 
   <requirements>
-    <requirement type="package" version="3.2.2">R</requirement>
+    <requirement type="package" version="3.3.1">R</requirement>    
     <requirement type="package">r-batch</requirement>
-    <requirement type="package" version="1.4.2">bioconductor-ropls</requirement>
+    <requirement type="package">bioconductor-ropls</requirement>
   </requirements>
   
   <stdio>
@@ -251,6 +251,12 @@
 NEWS
 ----
 
+CHANGES IN VERSION 2.2.6
+========================
+MINOR MODIFICATION
+
+Graphic: pool_CV inferior to 30%: pools with a NaN value are now counted as having a superior to 30% value (to avoid generating an NA metric value)
+
 CHANGES IN VERSION 2.2.4
 ========================
 
diff -r b4f5b5bc01dd -r 6d3b7b6573d8 qualitymetrics_script.R
--- a/qualitymetrics_script.R	Sat Aug 06 12:01:17 2016 -0400
+++ b/qualitymetrics_script.R	Fri Oct 21 12:56:22 2016 -0400
@@ -424,14 +424,16 @@
         text(1, 0.45, adj=0, cex = 1.1, labels = paste0("mean: ", signif(mean(datMN, na.rm=TRUE), 2)))
         text(1, 0.35, adj=0, cex = 1.1, labels = paste0("max: ", signif(max(datMN, na.rm=TRUE), 2)))
         if("sampleType" %in% colnames(samDF) &&
-           "pool" %in% samDF[, "sampleType"])
+           "pool" %in% samDF[, "sampleType"]) {
+            poolCvNanVl <- is.nan(varDF[, "pool_CV"])
             text(1,
                  0.25,
                  adj=0, cex = 1.1,
                  labels = paste0("pool CV < ",
                      round(thrVn["poolCv"] * 100), "%: ",
-                     round(sum(varDF[, "pool_CV"] < thrVn["poolCv"]) / nrow(varDF) * 100),
+                     round(sum(varDF[!poolCvNanVl, "pool_CV", drop = FALSE] < thrVn["poolCv"]) / nrow(varDF) * 100),
                      "%"))
+            }
 
         text(1, 0.1, adj=0, labels = paste0("Thresholds used in plots:"))
         text(1, 0, adj=0, labels = paste0("  p-value = ", thrVn["pvalue"]))