Mercurial > repos > davidecangelosi > pipe_t
changeset 18:2a6088c11d42 draft
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit d953cf83d97f579b4b03a30cd320f760d0ecdefc
| author | davidecangelosi |
|---|---|
| date | Tue, 28 May 2019 04:33:16 -0400 |
| parents | 81f51d722102 |
| children | 8503457bd0c4 |
| files | pipe-t.R pipe-t.xml |
| diffstat | 2 files changed, 79 insertions(+), 8 deletions(-) [+] |
line wrap: on
line diff
--- 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)
--- 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>