# HG changeset patch
# User yhoogstrate
# Date 1450282518 18000
# Node ID 7bb87a6bc4d5284c1aba043a31dd8e2192b4c2b7
# Parent  6c90a67a13fa82612973ea867538301dc4444756
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 77b660f5d221cc2c0725dc605a16805721d66dbc

diff -r 6c90a67a13fa -r 7bb87a6bc4d5 edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Mon Dec 14 05:10:49 2015 -0500
+++ b/edgeR_Differential_Gene_Expression.xml	Wed Dec 16 11:15:18 2015 -0500
@@ -288,6 +288,11 @@
   if(output_MDSplot_logFC != "/dev/null" || output_MDSplot_logFC_coordinates != "/dev/null" || output_hierarchical_clustering_plot != "/dev/null") {
     write("Calculating MDS plot (logFC method)",stdout())
     n_dim <- nrow(dge\$samples)
+    
+    if(n_dim >= nrow(dge\$counts)) {
+      n_dim <- 3
+    }
+    
     mds_distance_logFC <- plotMDS.DGEList(dge,top=500,labels=rep("",nrow(dge\$samples)),dim.plot=c(n_dim-2,n_dim-1))
     dev.off()# Kill it
     
diff -r 6c90a67a13fa -r 7bb87a6bc4d5 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Dec 14 05:10:49 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 16 11:15:18 2015 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="edger" version="3.11.0">
-        <repository changeset_revision="6ffda6224a37" name="package_r_edger_3_11_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="330f615d062e" name="package_r_edger_3_11_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     
     <package name="design_matrix_creator" version="1.0.0">