--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_get_mass_eic.xml	Sat Feb 07 22:02:00 2015 +0100
@@ -0,0 +1,117 @@
+<tool id="xcms_get_mass_eic" name="XCMS Get EICs"  version="0.0.4">
+	<description> Extracts EICs for a given list of masses</description>
+	<requirements>
+		<requirement type="package" version="3.1.1">R_bioc_metams</requirement>
+	</requirements>	
+	<command interpreter="Rscript">
+		xcms_get_mass_eic.r 
+	    $xsetData
+		$rtStart
+		$rtEnd
+		#if $massParameters.massParametersType == "window"
+			$massParameters.mzStart 
+			$massParameters.mzEnd
+			-1
+			"."
+		#else
+			-1
+			-1
+			"$massParameters.mzList" 
+			$massParameters.mzTolPpm
+		#end if  
+		"$sampleNames" 
+		$combineSamples
+		$rtPlotMode
+		$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" />
+	
+	<conditional name="massParameters">
+		<param name="massParametersType" type="select" size="50" label="Give masses as" >
+			<option value="list" selected="true">m/z list</option>
+			<option value="window" >m/z window</option>
+		</param>
+		<when value="list">
+			<param name="mzList" type="text" area="true" size="7x70" label="m/z list" 
+				help="Comma or line-separated list of m/z values for which to plot an EIC. One EIC will be plotted for each m/z given here.">
+				<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>
+			<param name="mzTolPpm" type="integer" size="10" value="5" label="m/z tolerance (ppm)"  />
+		</when>
+		<when value="window">
+			<param name="mzStart" type="float" value="" size="10" label="m/z start" help="Start of m/z window" />
+			<param name="mzEnd" type="float" value="" size="10"  label="m/z end" help="End of m/z window" />
+   		</when>
+	</conditional>		 
+	
+
+	<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. Here 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>
+	
+	<param name="combineSamples" type="select" size="50" label="Combine samples in EIC" 
+	       help="Combining samples means plot contains the combined EIC of a m/z in the different samples. When NOT combining, each plot 
+	       only contains the EIC of the m/z in the respectively given sample (the sample name from the sample list in the same position as the
+	       m/z in the m/z list.). Tip: use Yes for visualizing EIC of grouped masses (MsClust or CAMERA groups), use No for visualizing EICs of the same mass in 
+	       the different samples.">
+		<option value="No" selected="true">No</option>
+		<option value="Yes" >Yes</option>
+	</param>
+	<param name="rtPlotMode" type="select" size="50" label="RT plot mode" 
+	       help="Select whether EIC should be on original or raw Retention Time">
+		<option value="raw" selected="true">Raw</option>
+		<option value="corrected" >Corrected</option>
+	</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 will plot EICs for a given list of masses (or a mass window) using XCMS's getEIC method. 
+It produces a HTML report showing the EIC plots, one for each given mass. The figure below shows an example of such an EIC plot.
+ 
+.. image:: $PATH_TO_IMAGES/massEIC.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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