# HG changeset patch
# User davidecangelosi
# Date 1557740078 14400
# Node ID bc5697f4172072726868d35c6fa64bfdb9e6b417
# Parent  69f5c4d6e6bdc4a23cbeba19640d2ced5c5a761b
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 2c7880131d5a3ca88ddc31e2a52a12fa17774178

diff -r 69f5c4d6e6bd -r bc5697f41720 pipe-t.R
--- a/pipe-t.R	Fri May 10 10:49:09 2019 -0400
+++ b/pipe-t.R	Mon May 13 05:34:38 2019 -0400
@@ -24,12 +24,8 @@
 library(BBmisc)
 library(affy)
 library(psych)
-#library(gmp)
 library(zoo)
-library(nondetects)
 library(Hmisc)
-#library(missForest)
-#library(mice)
 })
 
 cat("\n R libraries...loaded!\n")
@@ -76,7 +72,7 @@
               filtnames<-args[23]
             }
         } else {
-          #mean, median, nondetects, cubic
+          #mean, median, cubic
             outputIMP<-args[18]
             DEAMethod<-args[19]
             if (DEAMethod=="ttest") {
@@ -121,7 +117,7 @@
               filtnames<-args[23]
             }
         } else {
-          #mean, median, nondetects, cubic
+          #mean, median, cubic
             outputIMP<-args[18]
             DEAMethod<-args[19]
             if (DEAMethod=="ttest") {
@@ -167,7 +163,7 @@
               filtnames<-args[23]
             }
         } else {
-          #mean, median, nondetects, cubic
+          #mean, median, cubic
             outputIMP<-args[18]
             DEAMethod<-args[19]
             if (DEAMethod=="ttest") {
@@ -216,7 +212,7 @@
           filtnames<-args[21]
         }
      } else {
-       #mean, median, nondetects, cubic 
+       #mean, median, cubic 
         outputIMP<-args[16]
         DEAMethod<-args[17]
           if (DEAMethod=="ttest") {
@@ -894,9 +890,6 @@
     "median"={
       exprs(qFiltNAs)<-impute(exprs(qFiltNAs),median)
     },
-    "nondetects"={
-      qFiltNAs <- qpcrImpute(qFiltNAs, outform=c("Single"),linkglm = c("logit"))
-    },
     stop("Enter something that switches me!")
 )
 
diff -r 69f5c4d6e6bd -r bc5697f41720 pipe-t.xml
--- a/pipe-t.xml	Fri May 10 10:49:09 2019 -0400
+++ b/pipe-t.xml	Mon May 13 05:34:38 2019 -0400
@@ -10,7 +10,6 @@
 <requirement type="package" version="1.11.0">r-bbmisc</requirement>
 <requirement type="package" version="1.8.4">r-psych</requirement>
 <requirement type="package" version="1.8_3">r-zoo</requirement>
-<requirement type="package" version="2.10.0">bioconductor-nondetects</requirement>
 <requirement type="package" version="4.1_1">r-hmisc</requirement>
 <requirement type="package" version="1.28.0">bioconductor-normqpcr </requirement>
 </requirements>
@@ -25,7 +24,7 @@
 
     #if str( $dn.condNorm.normMethod ) == "deltaCt":
         #if str( $dn.condNorm.deltamethod.format ) == "userdefined":
-          #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "nondetects" or str( $df.condImpute.format ) == "cubic":
+          #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic":
               #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
@@ -50,7 +49,7 @@
           #end if
         #end if
         #if str( $dn.condNorm.deltamethod.format ) == "genorm":
-            #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "nondetects" or str( $df.condImpute.format ) == "cubic":
+            #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic":
                 #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
@@ -75,7 +74,7 @@
             #end if
           #end if
           #if str( $dn.condNorm.deltamethod.format ) == "normfinder":
-              #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "nondetects" or str( $df.condImpute.format ) == "cubic":
+              #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic":
                   #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
@@ -101,7 +100,7 @@
             #end if
 
     #else
-      #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "nondetects" or str( $df.condImpute.format ) == "cubic":
+      #if str( $df.condImpute.format ) == "mestdagh" or str( $df.condImpute.format ) == "mean" or str( $df.condImpute.format ) == "median" or str( $df.condImpute.format ) == "cubic":
           #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
@@ -195,7 +194,6 @@
       <option value="mean">Mean</option>
       <option value="median">Median</option>
       <option value="cubic">Cubic Spline</option>
-      <option value="nondetects">Non-detects</option>
     </param>
     <when value="knn">
       <param name="k" type="integer" min="1" max="100" value="10" label="Type a number of neighbors to use by the KNN imputation method" />
@@ -268,35 +266,4 @@
 7) A txt file with a number statistics about the significance of each miR\gene
 ]]>
 </help>
-<citations>
-        <citation type="bibtex">
-    @Manual{HTqPCR,
-        title = {HTqPCR: Automated analysis of high-throughput qPCR data.},
-        author = {Heidi Dvinge, Paul Bertone},
-        year = {2009},
-        note = {R package version 1.36.0},
-        url = {http://bioconductor.org/packages/HTqPCR/},
-    }
-        </citation>
-        <citation type="bibtex">
-    @Manual{impute,
-        title = {Impute: Imputation for microarray data.},
-        author = {Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, Gilbert Chu},
-        year = {2018},
-        note = {R package version 1.56.0},
-        url = {http://bioconductor.org/packages/impute/},
-    }
-        </citation>
-        <citation type="bibtex">
-    @Manual{RankProd,
-        title = {RankProd:  Rank Product method for identifying differentially expressed
-genes with application in meta-analysis.},
-        author = {Francesco Del Carratore},
-        year = {2018},
-        note = {R package version 3.8.0},
-        url = {http://bioconductor.org/packages/RankProd/},
-    }
-        </citation>
-    </citations>
-
 </tool>