# HG changeset patch
# User yhoogstrate
# Date 1450087849 18000
# Node ID 6c90a67a13fa82612973ea867538301dc4444756
# Parent  5c94a732bd62a0821b91055a13ebab0c129ceaaf
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/edger_with_design_matrix commit 275a72ec0424e4e5d658d1bc8227077ea46f0fdc

diff -r 5c94a732bd62 -r 6c90a67a13fa edgeR_Differential_Gene_Expression.xml
--- a/edgeR_Differential_Gene_Expression.xml	Sat Dec 12 05:21:15 2015 -0500
+++ b/edgeR_Differential_Gene_Expression.xml	Mon Dec 14 05:10:49 2015 -0500
@@ -208,15 +208,22 @@
 
 for(i in 1:ncol(design_matrix)) {
   old <- design_matrix[,i]
-  design_matrix[,i] <- make.names(design_matrix[,i])
-  if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
-    print("Renaming of factors:")
-    print(old)
-    print("To:")
-    print(design_matrix[,i])
+  
+  if(any(grepl("^[0-9]+$", old, perl=TRUE) == FALSE)){
+    # Convert invalid names
+    design_matrix[,i] <- make.names(design_matrix[,i])
+    
+    # Print if names have been converted
+    if(paste(design_matrix[,i],collapse="\t") != paste(old,collapse="\t")) {
+      print("Renamed of factors:")
+      print(old)
+      print("To:")
+      print(design_matrix[,i])
+    }
+  } else {
+    # Only numerical factors: these are blocking / pairing factors
+    design_matrix[,i] <- as.numeric(design_matrix[,i])
   }
-  ## The following line seems to malfunction the script:
-  ##design_matrix[,i] <- as.factor(design_matrix[,i])
 }
 
 ## 1) In the expression matrix, you only want to have the samples described in the design matrix
@@ -720,6 +727,19 @@
             
             <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.significant.tabular.txt" />
         </test>
+        <test>
+            <param name="analysis_select" value="multi_factor" />
+            
+            <param name="expression_matrix" value="Differential_Gene_Expression/expression_matrix.tabular.txt" />
+            <param name="design_matrix" value="Differential_Gene_Expression/design_matrix.tabular.batch-effects.txt" />
+            
+            <param name="contrast" value="E-C"/>
+        
+            <param name="analysis_report_genes" value="all"/>
+            <param name="fdr" value="0.01" />
+            
+            <output name="output_count_edgeR" file="Differential_Gene_Expression/differentially_expressed_genes.batch-effects.tabular.txt" />
+        </test>
     </tests>
     
     <help>
diff -r 5c94a732bd62 -r 6c90a67a13fa test-data/Differential_Gene_Expression/design_matrix.tabular.batch-effects.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Differential_Gene_Expression/design_matrix.tabular.batch-effects.txt	Mon Dec 14 05:10:49 2015 -0500
@@ -0,0 +1,9 @@
+sample-name	Condition	Batch
+C1	C	1
+C2	C	1
+C3	C	2
+C4	C	2
+E1	E	1
+E2	E	1
+E3	E	2
+E4	E	2
diff -r 5c94a732bd62 -r 6c90a67a13fa test-data/Differential_Gene_Expression/differentially_expressed_genes.batch-effects.tabular.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Differential_Gene_Expression/differentially_expressed_genes.batch-effects.tabular.txt	Mon Dec 14 05:10:49 2015 -0500
@@ -0,0 +1,30 @@
+""	"genes"	"logFC"	"logCPM"	"LR"	"PValue"	"FDR"
+"15"	"RET"	1.95351498277649	13.2940435307943	70.7884298827703	3.9766237329402e-17	1.15322088255266e-15
+"24"	"HSPA8"	0.607097086193171	18.9380827005326	18.3388522248215	1.84897696413517e-05	0.000268101659799599
+"12"	"IFI44L"	-0.663271215486821	11.7020333673755	10.9083408215917	0.00095732231526494	0.00925411571422775
+"10"	"MYO18A"	-0.607030110998538	14.1586814058554	8.85972925087567	0.0029153081194653	0.0208760330354099
+"4"	"DDX11"	0.724160415576466	12.4597575302041	8.47565074268945	0.00359931604058791	0.0208760330354099
+"26"	"NR2C2AP"	0.538450796715875	12.9331552590697	6.96854404518889	0.00829549660040106	0.0400949002352718
+"19"	"RASSF3"	-0.323616221214522	12.4964626371138	3.7019217136962	0.05434983717189	0.225163611140687
+"3"	"DDX17"	-0.20201533346913	16.1804174471336	2.4240349611365	0.119486805704499	0.43313967067881
+"2"	"USP26"	-2.19888949506255	4.27316802151059	2.23930233943077	0.1345416719394	0.433523165138066
+"27"	"INADL"	-0.171504044976009	15.2186072712825	1.49672630947915	0.221175760548511	0.641409705590681
+"21"	"LYSMD3"	-0.194806526906794	13.32535006408	1.33073961519612	0.248673682102714	0.655594252816247
+"16"	"IQCG"	-0.208260226810614	10.1622224199572	0.967867000668835	0.3252127194599	0.785930738694759
+"6"	"SLC35D3"	0.789817686242913	4.62274850327991	0.638997348362095	0.424074105189856	0.922823270583707
+"14"	"KCNAB3"	0.224776816841962	7.85434240586327	0.477050454902194	0.489761385678098	0.922823270583707
+"20"	"FUT8"	-0.100266057923686	15.3006920075591	0.448528599960923	0.503034528215111	0.922823270583707
+"1"	"COMMD10"	0.129868119349192	12.8850203875481	0.43582621570193	0.509143873425494	0.922823270583707
+"9"	"TXLNB"	-0.183590716507963	7.2825391341052	0.269612199658876	0.603592030691037	0.990834288521076
+"28"	"TMEM31"	-0.231195333650393	6.16897757110336	0.252957033365721	0.615000592875151	0.990834288521076
+"17"	"C20orf118"	0.163495741844413	6.73904801103973	0.171566008065263	0.678723780532467	1
+"7"	"GLOD4"	-0.0679141042839315	13.8710260882794	0.154827011727691	0.693964522467115	1
+"22"	"LMOD3"	0.0791372844747401	7.60390982671528	0.0540610465986004	0.816141676483626	1
+"8"	"GIMAP7"	0.195152071961945	4.26623062002702	0.0194047958154413	0.889212222514442	1
+"23"	"HIPK1"	-0.00677640818725696	17.7957744498389	0.00305975315578166	0.955887483884316	1
+"11"	"ATG4B"	0.00473988666702576	13.5252482941211	0.000418258796557325	0.983683299966982	1
+"13"	"KHSRP"	-0.00184247000571017	14.7206397592923	0.000136964665301775	0.990662418229392	1
+"5"	"PTPN20B"	0	4.09631395702755	0	1	1
+"18"	"GPIHBP1"	0	4.09631395702755	0	1	1
+"25"	"TAS2R39"	0	4.09631395702755	0	1	1
+"29"	"GC"	0	4.09631395702755	0	1	1