# HG changeset patch
# User sblanck
# Date 1529914282 14400
# Node ID 25b828010ca9f80a42f866acf506913f787edbd2
# Parent  22e1325aaa88b41a463555f24de5e8acc1b533f4
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit bfd179bd7fb4796e21183e0e4de2fcf78ca35b7d

diff -r 22e1325aaa88 -r 25b828010ca9 ImportDataFromMatrix.R
--- a/ImportDataFromMatrix.R	Fri Jun 22 04:30:31 2018 -0400
+++ b/ImportDataFromMatrix.R	Mon Jun 25 04:11:22 2018 -0400
@@ -66,13 +66,10 @@
 colnames(conditions)=c("source_name_ch1","description")
 phenodata<-new("AnnotatedDataFrame",data=conditions)
 
-head(data)
-conditions
-
 eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation)
 
 if (normalization == "quantile") {
-	eset <- normalize.ExpressionSet.quantiles(eset, transfn="log2")
+	eset <- normalize.ExpressionSet.quantiles(eset, transfn="log")
 } else if (normalization == "log2") {
 	exprs(eset) = log2(exprs(eset)) 
 } 
diff -r 22e1325aaa88 -r 25b828010ca9 MetaRNAseq.xml
--- a/MetaRNAseq.xml	Fri Jun 22 04:30:31 2018 -0400
+++ b/MetaRNAseq.xml	Mon Jun 25 04:11:22 2018 -0400
@@ -70,10 +70,12 @@
 Given several DESeq2 results this tool runs a meta-analysis using the metaRNAseq R package.
 		
 **Inputs**
-At list 2 studies
-- Results of DESeq2 study
-- Number of replicate of the study			
+- At least 2 studies, and for each study
+	- Results of DESeq2 study
+	- Number of replicates of the study	
+- A FDR Threshold for a gene to be declared differentially expressed		
 	
+
 **Results**
 		
 - Venn Diagram or upsetR diagram (when the number of studies is greater than 2) summarizing the results of the meta-analysis
@@ -84,8 +86,8 @@
 	- Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis 
 	- DR (Integration-driven Discovery Rate) : corresponding proportion of IDD
 	- IRR (Integration-driven Revision) : corresponding proportion of Loss
-		
-- Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database.
+
+It also generates a text file containing summarization of the results of each single analysis and meta-analysis. Potential conflicts between single analyses are indicated by zero values in the "signFC" column. 
 ]]>
     </help>
 
diff -r 22e1325aaa88 -r 25b828010ca9 Recount.xml
--- a/Recount.xml	Fri Jun 22 04:30:31 2018 -0400
+++ b/Recount.xml	Mon Jun 25 04:11:22 2018 -0400
@@ -44,7 +44,7 @@
 
 **Results**
 	
-- Tabular file containing meta-data
+- Tabular file containing samples ID and samples conditions
 - One count file per sample
 ]]> 		
     </help>