Mercurial > repos > sblanck > smagexp
changeset 29:102e4ef8fed2 draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit 808ffb34e11a74cd2396e32868ea56f7ce8d83ff
| author | sblanck |
|---|---|
| date | Thu, 21 Jun 2018 07:57:16 -0400 |
| parents | 49ce6fbe11de |
| children | 4048dae6ace8 |
| files | MetaRNASeq.R MetaRNASeq_tpl.html MetaRNAseq.xml |
| diffstat | 3 files changed, 24 insertions(+), 10 deletions(-) [+] |
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--- 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)
--- 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 @@ <body> <table><tr><td> -<h2>###TITLE##</h2> -<img src='###VENN###' height="500" width=###WIDTH##><br/> +<h2>###TITLE###</h2> +<img src='###VENN###' height="500" width=###WIDTH###><br/> </td><td> </td></tr></table>
--- 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 @@ <command> - <![CDATA[ +<![CDATA[ Rscript ${__tool_directory__}/MetaRNASeq.R - --input "#for $input in $inputs# $input;$input.name, #end for#" + --input "#for $s in $studies: + ${s.input};${s.input.name};${s.nbreplicates}, + #end for +" + --fdr $fdr --result $top_table --htmloutput $result_html --htmloutputpath $result_html.extra_files_path - --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html - ]]> + --htmltemplate ${__tool_directory__}/MetaRNASeq_tpl.html + ]]> + </command> <inputs> - <param format="tabular" name="inputs" multiple="true" type="data" optional="false" label="Counts file" help="Must have the same number of row in each study. The experimental conditions must be specified in the header of each file"/> + <repeat name="studies" title="Study results" min="2" default="2" help="DESeq2 Result file and number of replicate of the study"> + <param format="tabular" name="input" multiple="false" type="data" optional="false" label="DESeq2 result file" help="Must have the same number of row in each study"/> + <param name="nbreplicates" type="integer" value="10" label="Number of replicates" help="Number of replicates of the study"/> + </repeat> + <param name="fdr" type="float" value="0.05" label="FDR" min="0" max="1" help="adjusted p-value threshold to be declared differentially expressed"/> </inputs> + <outputs> <data format="tabular" name="top_table" label="Summary of meta-analysis and single studie analysis from ${tool.name} on ${on_string}"/> <data format="html" name="result_html" label="Charts for ${tool.name} on ${on_string}"/>