# HG changeset patch
# User sblanck
# Date 1529589983 14400
# Node ID 2d7595c8041d46e564ce8e8d695bbc6b0e317a27
# Parent  2c0df656094a6ad44ff0114652c8afe1c04ceb86
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit d42088af604c5a01e1ccebba1d59f7a28a976f71

diff -r 2c0df656094a -r 2d7595c8041d MetaRNAseq.xml
--- a/MetaRNAseq.xml	Thu Jun 21 08:25:36 2018 -0400
+++ b/MetaRNAseq.xml	Thu Jun 21 10:06:23 2018 -0400
@@ -41,7 +41,7 @@
              <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"/>
+         <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>
 
 
diff -r 2c0df656094a -r 2d7595c8041d Recount.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Recount.R	Thu Jun 21 10:06:23 2018 -0400
@@ -0,0 +1,47 @@
+#!/usr/bin/env Rscript
+# setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+library("optparse")
+
+##### Read options
+option_list=list(
+		make_option("--id",type="character",default=NULL,help="GSE ID from GEO databse (required)"),
+		make_option("--report",type="character",default=NULL,help="Text file summarizing conditions of the experiment")
+
+);
+
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+
+if(is.null(opt$id)){
+	print_help(opt_parser)
+	stop("Recount id required.", call.=FALSE)
+}
+
+#loading libraries
+suppressPackageStartupMessages(require(GEOquery))
+
+studyID=opt$id
+reportFile=opt$report
+
+dir.create("./split", showWarnings = TRUE, recursive = FALSE)
+
+url <- download_study(studyID)
+load(file.path(studyID, 'rse_gene.Rdata'))
+rse <- scale_counts(rse_gene)
+counts=assay(rse)
+conditions=rse$title
+
+for (i in 1:ncol(counts))
+{
+	currentCount=as.data.frame(counts[,i])
+	sampleID=colnames(counts)[i]
+	colnames(currentCount)=sampleID
+	write.table(x=currentCount,file=paste0("./split/",sampleID,"_",conditions[i]),sep="\t",row.names = T, col.names = T)
+}
+
+write.table(as.data.frame(cbind(sampleID=colnames(counts),title=conditions)),quote = FALSE,col.names =TRUE, row.names=FALSE,file=reportFile,sep="\t")
\ No newline at end of file
diff -r 2c0df656094a -r 2d7595c8041d Recount.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Recount.xml	Thu Jun 21 10:06:23 2018 -0400
@@ -0,0 +1,52 @@
+<tool id="Recount" name="Recount" version="1.0.0">
+
+    <description>Get rna-seq count data with R recount Package</description>
+
+    <requirements>
+        <requirement type="package">bioconductor-recount</requirement>
+        <requirement type="package">r-optparse</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <regex match="Warning" source="both" level="warning"/>
+    </stdio>
+
+    <command>
+        <![CDATA[ 
+        Rscript --vanilla
+        ${__tool_directory__}/Recount.R 
+            --id ${RecountID}
+            --report ${Report}
+        ]]>
+    </command>
+
+    <inputs>
+        <param name="RecountID" type="text" size="12" optional="false" label="GEOQuery ID" help="">
+            <validator type="empty_field"/>
+        </param>
+     </inputs>
+
+    <outputs>
+    <data format="txt" name="report">
+        <discover_datasets pattern="__designation_and_ext__" directory="split" visible="true" />
+    </data>
+</outputs>
+
+    <tests>
+    </tests>
+
+    <help>
+<![CDATA[ 
+**What it does**     	
+
+This tool fetches RNA-seq count data directly from Recount project based on the recount bioconductor R package. Given an ID, it returns a small report 
+containing the metadata of the experiment. Il also generates one count file per sample.
+
+**Results**
+	
+- Tabular file containing meta-data
+- One count file per sample
+]]> 		
+    </help>
+
+</tool>