# 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 @@ - +