--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaMS/xcms_get_alignment_eic.xml	Thu Mar 19 12:22:23 2015 +0100
@@ -0,0 +1,73 @@
+<tool id="xcms_get_alignment_eic" name="XCMS Get Alignment EICs"  version="0.0.4">
+	<description> Extracts alignment EICs from feature alignment data</description>
+	<requirements>
+		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+	</requirements>	
+	<command interpreter="Rscript">
+		xcms_get_alignment_eic.r 
+	    $xsetData
+		$rtStart
+		$rtEnd
+		$minNrSamples
+		"$sampleNames" 
+		$htmlReportFile
+		$htmlReportFile.files_path
+		$outLogFile
+	</command>
+<inputs>
+	
+	<param name="xsetData" type="data" format="rdata" label="xset xcms data file" help="E.g. output data file resulting from METAMS run"/>
+	
+	
+	<param name="rtStart" type="integer" value="" size="10" label="RT start" help="Start of Retention Time region to plot" />
+	<param name="rtEnd" type="integer" value="" size="10"  label="RT end" help="End of Retention Time region to plot" />
+	
+	<param name="minNrSamples" type="integer" size="10" value="10" label="Minimum number of samples in which aligned feature should be found" help="Can also read this as: Minimum 
+	number of features in alignment. E.g. if set to 10, it means the alignment should consist of at least 10 peaks from 10 different samples aligned together." />
+	
+	<param name="sampleNames" type="text" area="true" size="10x70" label="List of sample names" 
+	value="sampleName1,sampleName2,etc"
+	help="Comma or line-separated list of sample names. Optional field where you can specify the subset of samples
+	to use for the EIC plots. NB: if your dataset has many samples, specifying a subset here can significantly speed up the processing time." >
+		<sanitizer>
+			<!-- this translates from line-separated to comma separated list, removes quotes  -->
+			<valid/>
+			<mapping initial="none">
+		    	<add source="&#10;" target=","/>
+		    	<add source="&#13;" target=""/>
+		    	<add source="&quot;" target=""/>
+ 			</mapping>
+		</sanitizer>	
+	</param>
+	
+	
+</inputs>
+<outputs>
+	<data name="outLogFile" format="txt" label="${tool.name} on ${on_string} - log (LOG)" hidden="True"/>
+	<data name="htmlReportFile" format="html" label="${tool.name} on ${on_string} - EIC(s) report (HTML)"/>
+</outputs>
+<tests>
+	<test>
+	</test>
+</tests>
+<help>
+
+.. class:: infomark
+ 
+This tool finds the alignments in the specified RT window and extracts alignment EICs from feature alignment data using XCMS's getEIC method. 
+It produces a HTML report showing the EIC plots and the mass list of each alignment. The figure below shows an example of such an EIC plot, showing also the difference between 
+two classes, with extra alignment information beneath it.
+ 
+.. image:: $PATH_TO_IMAGES/diffreport.png 
+
+Alignment id: 1709. m/z list of peaks in alignment:
+614.002922098482,613.998019830021,614.000382307519,613.998229980469,613.998229980469
+
+
+  </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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