view masscomb_dbsearch_mascot.xml @ 69:f6e879c9ce85

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<tool name="Mascot" id="masscomb_mascot" version="1.0.1">
	<description>MS/MS DB search</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 
	                    //////////////////////////
	   This part is a WORKAROUND for the Cytoscape X11 dependency problem, even when running 'headless':
	       export DISPLAY=:995;
	       ...TODO -> this is linux specific...follow issue fix on Cytoscape...perhaps we can add try/catch in python here (see http://www.unix.com/shell-programming-scripting/107334-how-use-catch-try-final-bash-script.html)
	       ...check how other tools do this  
	    -->
	<command interpreter="export DISPLAY=:995; java -jar">
	    SedMat_cli.jar -pl $inputMS -ppids $inputPedtipeList -out $outputData -mtol  $mtol -rttol $rttol -dataset $outputData.dataset.id
	</command>
	<inputs>
	 	<param name="inputMS" type="data" format="apml" label="MS data" />
	 	<param name="inputPedtipeList" type="data" format="apml" label="Peptide ID data from MS/MS" />
	 	<param name="outputFormat" type="select" label="Output format">
	    	<option value="apml">APML</option>
		</param>
		<param name="mtol" type="integer" size="10" value="50" label="Set m/z tolerance (ppm) " />
		<param name="rttol" type="integer" size="10" value="60" label="Set rention time tolerance (seconds) " />
	</inputs>
	<outputs>
	  <data name="outputData" format="apml"/>
	</outputs>
	<tests>
	  <!--  find out how to use -->
	  <test>
	    <param name="inputMS" value="testfile.pkl" ftype="pkl" />
	    <output name="outputData" file="testsedmatout.pkl" ftype="tabular" />
	  </test>
	</tests>
  <help>
  
.. class:: infomark
  
This tool matches MS and MS/MS results.
It can match peaks found in the MS spectra with the peptides found using the MS/MS spectra.
The result is the list of MS peaks annotated with peptides and proteins.

-----

**Output example**

This tools returns APML output, a Cytoscape network (.xgmml) of the matches and Retention Time plots (.pdf). 

  </help>
</tool>