--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaMS/xcms_differential_analysis.xml	Thu Mar 19 12:22:23 2015 +0100
@@ -0,0 +1,55 @@
+<tool id="xcms_differential_analysis" name="XCMS Differential Analsysis"  version="0.0.4">
+	<description> Runs xcms diffreport function for differential Analsysis</description>
+	<requirements>
+		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+	</requirements>	
+	<command interpreter="Rscript">
+		xcms_differential_analysis.r 
+	    $xsetData
+		"$class1"
+		"$class2"
+		$topcount
+		$outTable 
+		$htmlReportFile
+		$htmlReportFile.files_path
+		$outLogFile
+	</command>
+<inputs>
+	
+	<param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
+	
+	
+	<param name="class1" type="text" size="30" label="Class1 name" value="" help="Name of first class for the comparison"/>
+	<param name="class2" type="text" size="30" label="Class2 name" value="" help="Name of second class for the comparison"/>
+	
+	<param name="topcount" type="integer" size="10" value="10" label="Number of items to return" help="Top X differential items. E.g. if 10, it will return top 10 differential items." />
+	
+</inputs>
+<outputs>
+	<data name="outTable" format="tabular" label="${tool.name} on ${on_string} - Top differential items (TSV)"/>
+	<data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
+	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - differential report (HTML)"/>
+</outputs>
+<tests>
+	<test>
+	</test>
+</tests>
+<help>
+
+.. class:: infomark
+  
+Runs xcms diffreport for showing the most significant differences between two sets/classes of samples. This tool also creates extracted ion chromatograms (EICs) for 
+the most significant differences. The figure below shows an example of such an EIC.
+
+.. image:: $PATH_TO_IMAGES/diffreport.png 
+
+
+
+
+  </help>
+  <citations>
+        <citation type="doi">10.1021/ac051437y</citation> <!-- example 
+        see also https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+        -->
+   </citations>
+</tool>
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