--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/masscomb_visual_mspicture.xml	Wed Jan 08 11:34:51 2014 +0100
@@ -0,0 +1,87 @@
+<tool name="MsPicture" id="masscomb_mspicture" version="1.0.1">
+	<description>MS data view</description>
+	<!-- 
+	   For remote debugging start you listener on port 8000 and use the following as command interpreter:
+	       java -jar -Xdebug -Xrunjdwp:transport=dt_socket,address=D0100564.wurnet.nl:8000 
+	-->    
+	<command interpreter="java -jar">
+	    MassComb.jar -action MSPICTURE 
+	    -outputFile $html_file 
+	    -picturesPath $html_file.files_path 
+	    -fileGrouping $fileType.type
+	    #if $fileType.type == "single"
+	    	-inputFile $fileType.inputFormatType.inputFile
+	    	-inputFormat $fileType.inputFormatType.inputFormat
+        #elif $fileType.type == "fileSet"
+	    	-inputFile $fileType.inputFile
+        #end if
+        -parametersFile $parametersFile
+		
+	    </command>
+<inputs>
+  <conditional name="fileType">
+    <param name="type" type="select" label="select MS/MS input type">
+      <option value="single" selected="true">single-File</option>
+      <option value="fileSet">fileSet</option>
+    </param>
+    <when value="single">
+      <conditional name="inputFormatType">
+      	<param name="inputFormat" type="select" label="inputFormat">
+	    		<option value="mzml" selected="true">mzml</option>
+				<option value="mzxml">mzxml</option>
+	    		<option value="apml">apml</option>
+		</param>
+		<when value="mzxml">
+      		<param name="inputFile" type="data" format="mzxml" label="MS input file (mzXML)"/>
+      	</when>
+      	<when value="mzml">
+      		<param name="inputFile" type="data" format="mzml" label="MS input file (mzml)"/>
+      	</when>
+      	<when value="apml">
+      		<param name="inputFile" type="data" format="apml" label="MS or MS/MS input file (APML)"/>
+      	</when>
+      </conditional>
+    </when>
+    <when value="fileSet">
+      <param name="inputFile" type="data" format="prims.fileset.zip" label="input file"/>
+    </when>
+  </conditional>
+
+  <param name="data_type" type="select" label="Data type" help=""> 
+   	    <option value="LC-MS">LC-MS</option>
+   	    <option value="LC-MS/MS">LC-MS/MS</option>
+  </param>
+
+  <param name="gray_scale" type="select" display="checkboxes" multiple="True" label="Use gray scale" help=""> 
+   	    <option value="Yes">Yes</option>
+  </param>
+
+</inputs>
+<configfiles>
+<configfile name="parametersFile">&lt;?xml version="1.0" encoding="UTF-8"?&gt;
+&lt;tns:Program xmlns:tns="http://masscomb.pri.com/toolparameters/" name="MsPictureWrapper" program="MsPictureWrapper"&gt;
+	&lt;Files/&gt;
+	&lt;Parameters&gt;
+		  &lt;Attribute attributeName="toolLocation" value="/home/lukas007/bin/" type="Unknown" description=""/&gt;
+		  &lt;Attribute attributeName="gray_scale" toolSpecificName="--grey" value="${gray_scale}" type="Unknown" description=""/&gt;
+		  &lt;Attribute attributeName="data_type" value="${data_type}" type="Unknown" description=""/&gt;
+	&lt;/Parameters&gt;
+&lt;/tns:Program&gt;  
+</configfile>
+</configfiles>
+<outputs>
+	<data format="html" name="html_file" />
+</outputs>
+<tests>
+	<test>
+	</test>
+</tests>
+<help>
+
+.. class:: infomark
+  
+This tool displays the MS data using ProteoWizard's msPicture tool
+
+
+</help>
+</tool>
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