# HG changeset patch # User sblanck # Date 1529582236 14400 # Node ID 102e4ef8fed297bf699afa28e8cf49d9db895bd6 # Parent 49ce6fbe11de5463f90c6f0c6539c9b3b07365c1 planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 808ffb34e11a74cd2396e32868ea56f7ce8d83ff diff -r 49ce6fbe11de -r 102e4ef8fed2 MetaRNASeq.R --- a/MetaRNASeq.R Thu Jun 21 04:28:19 2018 -0400 +++ b/MetaRNASeq.R Thu Jun 21 07:57:16 2018 -0400 @@ -10,6 +10,7 @@ ##### Read options option_list=list( make_option("--input",type="character",default="NULL",help="list of rdata objects containing eset objects"), + make_option("--fdr",type="character",default=NULL,help="Adjusted p-value threshold to be declared differentially expressed"), make_option("--result",type="character",default=NULL,help="text file containing result of the meta-analysis"), make_option("--htmloutput",type="character",default=NULL,help="Output html report"), make_option("--htmloutputpath",type="character",default="NULL",help="Path of output html report"), @@ -35,20 +36,23 @@ listfiles=vector() listfilenames=vector() +nbreplicates=vector() for (i in 1:length(listInput)) { inputFileInfo <- unlist( strsplit( listInput[i], ';' ) ) listfiles=c(listfiles,inputFileInfo[1]) listfilenames=c(listfilenames,inputFileInfo[2]) + nbreplicates[i]=inputFileInfo[3] } + outputfile <- opt$result result.html = opt$htmloutput html.files.path=opt$htmloutputpath result.template=opt$htmltemplate -alpha=0.05 +alpha=opt$fdr #print(comparison) @@ -160,7 +164,7 @@ #nrep=c(length(listFiles)) -invnormcomb<-invnorm(rawpval, nrep=c(8,8), BHth=alpha) +invnormcomb<-invnorm(rawpval, nrep=nbreplicates, BHth=alpha) #DE[["fishercomb"]]<-ifelse(fishcomb$adjpval<=alpha,1,0) #DE[["invnormcomb"]]<-ifelse(invnormcomb$adjpval<=alpha,1,0) @@ -229,7 +233,7 @@ htmlfile=gsub(x=htmlfile,pattern = "###INVSUMMARYJSON###",replacement = summaryinvnormjson, fixed = TRUE) htmlfile=gsub(x=htmlfile,pattern = "###VENN###",replacement = vennFilename, fixed = TRUE) htmlfile=gsub(x=htmlfile,pattern = "###WIDTH##",replacement = as.character(width), fixed = TRUE) -htmlfile=gsub(x=htmlfile,pattern = "###TITLE##",replacement = as.character(width), fixed = TRUE) +htmlfile=gsub(x=htmlfile,pattern = "###TITLE##",replacement = title, fixed = TRUE) write(htmlfile,result.html) #library(VennDiagram) diff -r 49ce6fbe11de -r 102e4ef8fed2 MetaRNASeq_tpl.html --- a/MetaRNASeq_tpl.html Thu Jun 21 04:28:19 2018 -0400 +++ b/MetaRNASeq_tpl.html Thu Jun 21 07:57:16 2018 -0400 @@ -139,8 +139,8 @@

###TITLE##

###TITLE###

diff -r 49ce6fbe11de -r 102e4ef8fed2 MetaRNAseq.xml --- a/MetaRNAseq.xml Thu Jun 21 04:28:19 2018 -0400 +++ b/MetaRNAseq.xml Thu Jun 21 07:57:16 2018 -0400 @@ -20,21 +20,31 @@ - + --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html + ]]> + - + + + + + +