diff MetaRNAseq.xml @ 0:27ffdb495852 draft default tip

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MetaRNAseq.xml	Wed Apr 13 07:40:02 2016 -0400
@@ -0,0 +1,53 @@
+<tool id="metarnaseq" name="metaRNASeq">
+	<description>metaRNASeq wrapper</description>
+	<requirements>
+	  <container type="docker">sblanck/testtool:latest</container>
+	</requirements>
+	<command>
+
+		/galaxy-tools/stderr_wrapper.py Rscript 
+		/galaxy-tools/transcriptomics/MetaRNASeq/MetaRNASeq.R 
+		#for $currentInput in $inputList
+        	"${currentInput}"
+			"${currentInput.name}"	
+		 #end for	
+			$comparison 
+			$method 
+			$mod 
+			$top_table 
+			$diagnostic_html 
+			"$diagnostic_html.files_path"
+		/galaxy-tools/transcriptomics/MetaRNAseq/MetaRNASeq_tpl.html	
+	</command>
+
+	<inputs>
+		<param format="tabular" name="inputList" 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"/>
+
+		<param name="method" type="select" label="Compute dispersion method" help="">
+			<option value="pooled">Pooled</option>
+			<option value="pooled-CR">Pooled-CR</option>
+			<option value="per-condition">Per-condition</option>
+			<option value="blind">Blind</option>
+		</param>
+		<param name="mod" type="select" label="Compute dispersion sharingmod" help="">
+			<option value="maximum">Maximum</option>
+			<option value="fit-only">Fit-only</option>
+			<option value="gene-est-only">Gene-est-only</option>
+		</param>
+
+		<param name="comparison" type="text" size="30" optional="false" label="Comparison type" help="A comma separated tuple (no spaces) of the comparison you want to do.  Must use the names from the Column Types list.  E.g. comparing kidney to liver: kidney,liver.  Comparing liver to kidney: liver,kidney">
+			<validator type="empty_field"/>
+			<validator type="regex" message="Must be a comma-separated tuple with no spaces">^\w+,\w+$</validator>
+		</param>
+	</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="diagnostic_html" label="Charts for ${tool.name} on ${on_string}"/>
+	</outputs>
+
+	<help>
+		NOTE: This metaRNASeq Galaxy tool can only be run on counts files. 
+	</help>
+
+</tool>