# HG changeset patch
# User yhoogstrate
# Date 1441108862 14400
# Node ID f06dceb5b9662d2469131594f7a8ba36e43aab58
# Parent  5d7efbca6c753791390af8bd25de1622ce95c03a
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 097f2974042345a231e431299a031f236f3eb689-dirty

diff -r 5d7efbca6c75 -r f06dceb5b966 edgeR_Concatenate_Expression_Matrices.xml
--- a/edgeR_Concatenate_Expression_Matrices.xml	Tue Sep 01 07:54:09 2015 -0400
+++ b/edgeR_Concatenate_Expression_Matrices.xml	Tue Sep 01 08:01:02 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="concatenate_expression_matrices" name="edgeR: Concatenate Expression Matrices" version="1.0.0">
+<tool id="concatenate_expression_matrices" name="edgeR: Concatenate Expression Matrices" version="1.0.0.b">
     <description>Create a full expression matrix by selecting the desired columns from specific count tables</description>
     
     <macros>
diff -r 5d7efbca6c75 -r f06dceb5b966 edgeR_Convert_DGE_Table_to_Bedgraph.xml
--- a/edgeR_Convert_DGE_Table_to_Bedgraph.xml	Tue Sep 01 07:54:09 2015 -0400
+++ b/edgeR_Convert_DGE_Table_to_Bedgraph.xml	Tue Sep 01 08:01:02 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-    <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0">
+    <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0.b">
     <description>EdgeR's "differentially expressed genes" table to bedgraph(s)</description>
     
     <macros>
diff -r 5d7efbca6c75 -r f06dceb5b966 edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Tue Sep 01 07:54:09 2015 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Tue Sep 01 08:01:02 2015 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.a">
+<tool id="edger_dge" name="edgeR: Differential Gene(Expression) Analysis" version="3.11.0.b">
     <description>RNA-Seq gene expression analysis using edgeR (R package)</description>
     
     <macros>
@@ -101,9 +101,6 @@
             
             $output_format_images
             '
-            #if $output_R:
-                > $output_R
-            #end if
     </command>
     
     <configfiles>
@@ -238,7 +235,7 @@
       diff_x <- abs(max(mds_distance_logFC\$x)-min(mds_distance_logFC\$x))
       diff_y <-(max(mds_distance_logFC\$y)-min(mds_distance_logFC\$y))
       plot(c(min(mds_distance_logFC\$x),max(mds_distance_logFC\$x) + 0.45 * diff_x), c(min(mds_distance_logFC\$y) - 0.05 * diff_y,max(mds_distance_logFC\$y) + 0.05 * diff_y), main="edgeR logFC-MDS Plot on top 500 genes",type="n", xlab="Leading logFC dim 1", ylab="Leading logFC dim 2")
-      mds_distance_logFC(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20)
+      points(mds_distance_logFC\$x,mds_distance_logFC\$y,pch=20)
       text(mds_distance_logFC\$x, mds_distance_logFC\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
       rm(diff_x,diff_y)
       
@@ -270,7 +267,7 @@
     diff_x <- abs(max(mds_distance_BCV\$x)-min(mds_distance_BCV\$x))
     diff_y <- (max(mds_distance_BCV\$y)-min(mds_distance_BCV\$y))
     plot(c(min(mds_distance_BCV\$x),max(mds_distance_BCV\$x) + 0.45 * diff_x), c(min(mds_distance_BCV\$y) - 0.05 * diff_y,max(mds_distance_BCV\$y) + 0.05 * diff_y), main="edgeR BCV-MDS Plot",type="n", xlab="Leading BCV dim 1", ylab="Leading BCV dim 2")
-    mds_distance_BCV(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20)
+    points(mds_distance_BCV\$x,mds_distance_BCV\$y,pch=20)
     text(mds_distance_BCV\$x, mds_distance_BCV\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
     rm(diff_x,diff_y)
     
@@ -432,8 +429,6 @@
             <option value="make_output_PValue_distribution_plot">P-Value distribution plot</option>
             <option value="make_output_hierarchical_clustering_plot">Hierarchical custering</option>
             <option value="make_output_heatmap_plot">Heatmap</option>
-            
-            <option value="make_output_R_stdout">R stdout</option>
             <option value="make_output_RData_obj">R Data object</option>
         </param>