<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>