# HG changeset patch
# User davidecangelosi
# Date 1559032396 14400
# Node ID 2a6088c11d42db4d295d0bcc70b52a222b517942
# Parent  81f51d7221021ef89073e6fc1939f164548ecec3
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc

diff -r 81f51d722102 -r 2a6088c11d42 pipe-t.R
--- a/pipe-t.R	Fri May 24 10:49:05 2019 -0400
+++ b/pipe-t.R	Tue May 28 04:33:16 2019 -0400
@@ -58,7 +58,7 @@
           outputIMP<-args[20]
 
           DEAMethod<-args[21]
-          if (DEAMethod=="ttest") {
+          if (DEAMethod=="ttest" || DEAMethod=="wtest") {
               alternative<- args[22]
               paired<-args[23]
               replicates<- args[24]
@@ -75,7 +75,7 @@
           #mean, median, cubic
             outputIMP<-args[18]
             DEAMethod<-args[19]
-            if (DEAMethod=="ttest") {
+            if (DEAMethod=="ttest" || DEAMethod=="wtest") {
                 alternative<- args[20]
                 paired<-args[21]
                 replicates<- args[22]
@@ -103,7 +103,7 @@
           outputIMP<-args[20]
 
           DEAMethod<-args[21]
-          if (DEAMethod=="ttest") {
+          if (DEAMethod=="ttest" || DEAMethod=="wtest") {
               alternative<- args[22]
               paired<-args[23]
               replicates<- args[24]
@@ -120,7 +120,7 @@
           #mean, median, cubic
             outputIMP<-args[18]
             DEAMethod<-args[19]
-            if (DEAMethod=="ttest") {
+            if (DEAMethod=="ttest" || DEAMethod=="wtest") {
                 alternative<- args[20]
                 paired<-args[21]
                 replicates<- args[22]
@@ -149,7 +149,7 @@
           outputIMP<-args[20]
 
           DEAMethod<-args[21]
-          if (DEAMethod=="ttest") {
+          if (DEAMethod=="ttest" || DEAMethod=="wtest") {
               alternative<- args[22]
               paired<-args[23]
               replicates<- args[24]
@@ -166,7 +166,7 @@
           #mean, median, cubic
             outputIMP<-args[18]
             DEAMethod<-args[19]
-            if (DEAMethod=="ttest") {
+            if (DEAMethod=="ttest" || DEAMethod=="wtest") {
                 alternative<- args[20]
                 paired<-args[21]
                 replicates<- args[22]
@@ -198,7 +198,7 @@
 
       DEAMethod<-args[19]
      
-      if (DEAMethod=="ttest") {
+      if (DEAMethod=="ttest" || DEAMethod=="wtest") {
           alternative<- args[20]
           paired<-args[21]
           replicates<- args[22]
@@ -215,7 +215,7 @@
        #mean, median, cubic 
         outputIMP<-args[16]
         DEAMethod<-args[17]
-          if (DEAMethod=="ttest") {
+          if (DEAMethod=="ttest" || DEAMethod=="wtest") {
             alternative<- args[18]
             paired<-args[19]
             replicates<- args[20]
@@ -868,6 +868,23 @@
 
 write.table(exprs(qFiltNAs), file=outputRemaining, quote=FALSE,  row.names=TRUE, col.names=TRUE, sep = "\t")
 
+switch(DEAMethod,
+    "ttest"={
+     #Differential expression analysis (paired t test+BH). Returns Fold change in linear scale.
+      DEG<-ttestCtData(qFiltNAs, groups = files$Treatment, alternative = alternative, paired = ifelse(paired=="TRUE", TRUE, FALSE), replicates =ifelse(replicates=="TRUE", TRUE, FALSE), sort=ifelse(sort=="TRUE", TRUE, FALSE), stringent=ifelse(stringent=="TRUE", TRUE, FALSE), p.adjust=padjust)
+      write.table(DEG, file=outputDEA, quote=FALSE,  row.names=TRUE, col.names=TRUE,sep = "\t")
+    },
+    "wtest"={
+      DEG<-mannwhitneyCtData(qFiltNAs, groups = files$Treatment, alternative = alternative, paired = ifelse(paired=="TRUE", TRUE, FALSE), replicates =ifelse(replicates=="TRUE", TRUE, FALSE), sort=ifelse(sort=="TRUE", TRUE, FALSE), stringent=ifelse(stringent=="TRUE", TRUE, FALSE), p.adjust=padjust)
+      write.table(DEG, file=outputDEA, quote=FALSE,  row.names=TRUE, col.names=TRUE,sep = "\t")
+    },
+    "rp"={
+      DEG<-RP(exprs(qFiltNAs), as.numeric(pData(qFiltNAs)$Treatment)-1, num.perm = 1000,logged = TRUE, gene.names = featureNames(qFiltNAs), huge=TRUE, plot = FALSE, rand = 123)
+ write.table(DEG[1:5], file=outputDEA, quote=FALSE,  row.names=TRUE, col.names=TRUE,sep = "\t")
+    },
+    stop("Enter something that switches me!")
+)
+
 if (DEAMethod=="ttest") {
  #Differential expression analysis (paired t test+BH). Returns Fold change in linear scale.
  DEG<-ttestCtData(qFiltNAs, groups = files$Treatment, alternative = alternative, paired = ifelse(paired=="TRUE", TRUE, FALSE), replicates =ifelse(replicates=="TRUE", TRUE, FALSE), sort=ifelse(sort=="TRUE", TRUE, FALSE), stringent=ifelse(stringent=="TRUE", TRUE, FALSE), p.adjust=padjust)
diff -r 81f51d722102 -r 2a6088c11d42 pipe-t.xml
--- a/pipe-t.xml	Fri May 24 10:49:05 2019 -0400
+++ b/pipe-t.xml	Tue May 28 04:33:16 2019 -0400
@@ -28,6 +28,9 @@
               #if str( $de.condDEA.method ) == "ttest":
                   Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
               #end if
+              #if str( $de.condDEA.method ) == "wtest":
+                  Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers" $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
+              #end if
               #if str( $de.condDEA.method ) == "rp":
                   Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers"  $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
               #end if
@@ -40,6 +43,9 @@
               #if str( $de.condDEA.method ) == "ttest":
                     Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers"  $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
               #end if
+              #if str( $de.condDEA.method ) == "wtest":
+                    Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers"  $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
+              #end if
               #if str( $de.condDEA.method ) == "rp":
                     Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" "$dn.condNorm.deltamethod.normalizers"  $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
               #end if
@@ -53,6 +59,9 @@
                 #if str( $de.condDEA.method ) == "ttest":
                     Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
                 #end if
+                 #if str( $de.condDEA.method ) == "wtest":
+                    Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
+                #end if
                 #if str( $de.condDEA.method ) == "rp":
                     Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
                 #end if
@@ -65,6 +74,9 @@
                 #if str( $de.condDEA.method ) == "ttest":
                       Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm  $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
                 #end if
+                 #if str( $de.condDEA.method ) == "wtest":
+                      Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm  $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
+                #end if
                 #if str( $de.condDEA.method ) == "rp":
                       Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhkgenorm  $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
                 #end if
@@ -78,6 +90,9 @@
                   #if str( $de.condDEA.method ) == "ttest":
                       Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
                   #end if
+                   #if str( $de.condDEA.method ) == "wtest":
+                      Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
+                  #end if
                   #if str( $de.condDEA.method ) == "rp":
                       Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
                   #end if
@@ -90,6 +105,9 @@
                   #if str( $de.condDEA.method ) == "ttest":
                         Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder  $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
                   #end if
+                  #if str( $de.condDEA.method ) == "wtest":
+                        Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder  $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
+                  #end if
                   #if str( $de.condDEA.method ) == "rp":
                         Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod "$dn.condNorm.deltamethod.format" $dn.condNorm.deltamethod.minhknormfinder  $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
                   #end if
@@ -104,6 +122,9 @@
           #if str( $de.condDEA.method ) == "ttest":
               Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
           #end if
+           #if str( $de.condDEA.method ) == "wtest":
+              Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
+          #end if
           #if str( $de.condDEA.method ) == "rp":
               Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
           #end if
@@ -116,6 +137,9 @@
           #if str( $de.condDEA.method ) == "ttest":
                 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
           #end if
+          #if str( $de.condDEA.method ) == "wtest":
+                Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $de.condDEA.alternative $de.condDEA.paired $de.condDEA.replicates $de.condDEA.sort $de.condDEA.stringent $de.condDEA.padjust $galaxy_output7 "$df.filtname";
+          #end if
           #if str( $de.condDEA.method ) == "rp":
                 Rscript $__tool_directory__/pipe-t.R $dp.files "$dp.formatFile" $dp.n $galaxy_output1 "$__tool_directory__/Symlink" $dc.Ctmin $dc.Ctmax $dc.flag $galaxy_output2 $dn.condNorm.normMethod $galaxy_output3 $galaxy_output4 $df.percent $galaxy_output5 $df.condImpute.format $df.condImpute.k $df.condImpute.maxp $galaxy_output6 $de.condDEA.method $galaxy_output7 "$df.filtname";
           #end if
@@ -204,7 +228,9 @@
   <section name="de" title="Differential expression analysis" expanded="true">
     <conditional name="condDEA">
       <param name="method" type="select"  label="Select one of the methods from the list below or NONE.">
+        
         <option value="ttest" selected="true">T-test and fold change</option>
+        <option value="wtest" selected="true"> Two sample Wilcoxon test and fold change</option>
         <option value="rp">Rank Product (Only for unpaired data)</option>
         <option value="none">NONE</option>
       </param>
@@ -236,6 +262,34 @@
           <option value="bonferroni">Bonferroni</option>
         </param>
       </when>
+      <when value="wtest">
+        <param name="alternative" type="select"  label="Select one of the types of alternative hypothesis to assess significance.">
+          <option value="two.sided" selected="true">Two sided</option>
+          <option value="greater">Greater</option>
+          <option value="less">Lower</option>
+        </param>
+        <param name="paired" type="select" label="Select TRUE if you want a paired analysis." help="Pairing of samples will follow the order of the sampleNames in the input file">
+            <option value="TRUE" >TRUE</option>
+            <option value="FALSE" selected="true">FALSE</option>
+        </param>
+        <param name="replicates" type="select" label="Select TRUE if you have replicated transcripts in your data" help="If replicated transcripts are present in the data, the statistics will be calculated once for each replicated transcript, rather than separately.">
+            <option value="TRUE" selected="true">TRUE</option>
+            <option value="FALSE" >FALSE</option>
+        </param>
+        <param name="sort" type="select" label="Select TRUE if you want that output file is sorted by increasing order of p-value?" help="">
+            <option value="TRUE" selected="true">TRUE</option>
+            <option value="FALSE" >FALSE</option>
+        </param>
+        <param name="stringent" type="select" label="Select TRUE to admit more stringent analysis." help=" If stringent is TRUE any unreliable or undetermined measurements among technical and
+biological replicates will result in the final result being Undetermined. If stringent is FALSE result will be OK unless at least half of the Ct values for a given gene are unreliable/undetermined.">
+            <option value="TRUE" selected="true">TRUE</option>
+            <option value="FALSE" >FALSE</option>
+        </param>
+        <param name="padjust" type="select"  label="Select one of the methods for adjusting pvalues in case of multiple hypothesis testing">
+          <option value="BH" selected="true">Benjamini-Hochberg</option>
+          <option value="bonferroni">Bonferroni</option>
+        </param>
+      </when>
       <when value="rp">
       </when>
     </conditional>