# HG changeset patch
# User yhoogstrate
# Date 1441097639 14400
# Node ID dfebd3787276d8431c8c68c640ec0a1fe1070f19
# Parent  a02794bb9073251b4186f9b941b18cbda3ccab3a
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 2700e500a4fb135a20ede7d52221a9d31f1aaa5e-dirty

diff -r a02794bb9073 -r dfebd3787276 README.rst
--- a/README.rst	Tue Sep 01 04:45:24 2015 -0400
+++ b/README.rst	Tue Sep 01 04:53:59 2015 -0400
@@ -19,9 +19,11 @@
 
 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
 
-More tools by the Translational Research IT (TraIT) project can be found in the following repository:
+More tools by the Translational Research IT (TraIT) project can be found in the following toolsheds:
 
-http://toolshed.dtls.nl/
+http://toolshed.g2.bx.psu.edu
+
+http://testtoolshed.g2.bx.psu.edu/
 
 License
 -------
diff -r a02794bb9073 -r dfebd3787276 edgeR_Design_from_Expression_Matrix.xml
--- a/edgeR_Design_from_Expression_Matrix.xml	Tue Sep 01 04:45:24 2015 -0400
+++ b/edgeR_Design_from_Expression_Matrix.xml	Tue Sep 01 04:53:59 2015 -0400
@@ -92,7 +92,6 @@
         <data format="tabular" name="design_matrix" label="Design matrix" />
     </outputs>
     
-    
     <tests>
         <test>
             <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" />
diff -r a02794bb9073 -r dfebd3787276 edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Tue Sep 01 04:45:24 2015 -0400
+++ b/edgeR_Differential_Gene_Expression.xml	Tue Sep 01 04:53:59 2015 -0400
@@ -236,7 +236,7 @@
     
     
     diff_x <- abs(max(points\$x)-min(points\$x))
-    diff_y &lt;-(max(points\$y)-min(points\$y))
+    diff_y <-(max(points\$y)-min(points\$y))
     plot(c(min(points\$x),max(points\$x) + 0.45 * diff_x), c(min(points\$y) - 0.05 * diff_y,max(points\$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")
     points(points\$x,points\$y,pch=20)
     text(points\$x, points\$y,rownames(dge\$samples),cex=1.25,col="gray",pos=4)
@@ -329,7 +329,7 @@
       }
       
       with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
-      with(subset(etable, FDR &lt; fdr), points(logCPM, logFC, pch=20, col="red"))
+      with(subset(etable, FDR < fdr), points(logCPM, logFC, pch=20, col="red"))
       abline(h=c(-1,1), col="blue")
       dev.off()
     }
@@ -348,8 +348,8 @@
         bitmap(output_PValue_distribution_plot,type="png16m",width=14,height=14)
       }
       
-      expressed_genes <- subset(etable, PValue &lt; 0.99)
-      h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (&lt; 0.99)")
+      expressed_genes <- subset(etable, PValue < 0.99)
+      h <- hist(expressed_genes\$PValue,breaks=nrow(expressed_genes)/15,main="Binned P-Values (< 0.99)")
       center <- sum(h\$counts) / length(h\$counts)
       lines(c(0,1),c(center,center),lty=2,col="red",lwd=2)
       k <- ksmooth(h\$mid, h\$counts)