X!Tandem and PeptideProphet on the Grid

Script

import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;

	    	    DocumentBuilder db = DocumentBuilderFactory.newInstance().newDocumentBuilder();
	    	    InputSource is = new InputSource();
	    	    is.setCharacterStream(new StringReader(input));

	    	    Document doc = db.parse(is);
	    		String nodeName = doc.getDocumentElement().getNodeName();
	    		NodeList biomlList = doc.getElementsByTagName("bioml");
	    		System.out.println(biomlList.toString());
	    		for (int i = 0; i < biomlList.getLength(); i++) {
	    			 
	    			   Node node = biomlList.item(i);
	    			   if (node.getNodeType() == Node.ELEMENT_NODE) {
	    			      Element bioml = (Element) node;
	    			      NodeList noteList = bioml.getElementsByTagName("note");
	    			     
	    			      for (int j = 0; j < noteList.getLength(); j++) {
	    			    	  Node note = noteList.item(j);
	    			    	  if (note.getNodeType() == Node.ELEMENT_NODE) {
	    			 	    	 
	    	    			      Element el = (Element) note;
	    	    			      String attribute1 = el.getAttribute("label");
	    	    			    if(attribute1.equals("spectrum, parent monoisotopic mass error minus")){
	    	    			      el.getFirstChild().setNodeValue(minus);
	    	    			    }
	    	    			    if(attribute1.equals("spectrum, parent monoisotopic mass error plus")){
		    	    			      el.getFirstChild().setNodeValue(plus);
		    	    			    }
	    	    			    if(attribute1.equals("spectrum, parent monoisotopic mass isotope error")){
		    	    			      el.getFirstChild().setNodeValue(error);
		    	    			    }
					    if(attribute1.equals("scoring, maximum missed cleavage sites")){
		    	    			      el.getFirstChild().setNodeValue(cleavage);
		    	    			    }

					    if(attribute1.equals("protein, cleavage semi")){
							int s= Integer.parseInt(semi);
							if(s==0){

							 el.getParentNode().removeChild(el);	
							}
		    	    			     
		    	    			    }
	    	    			      
	    			    	  }
	    			      }
	    	 
	    			   }
	    		}
TransformerFactory transformerFactory = TransformerFactory.newInstance();
	    		Transformer transformer = transformerFactory.newTransformer();
	    		DOMSource source = new DOMSource(doc);
File input_file = new File(directory+"params.xml");
	    		StreamResult result = new StreamResult(input_file);
	    		transformer.transform(source, result);

Script

// This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA). 
// Copyright© 2012 Yassene Mohammed
// Please send your feedback, questions, comments and suggestions for improvement to y.mohammed@lumc.nl
// 25 June 2012
// Yassene

String stdout = "beanshell \n";

String fullcommand = "java -jar " + mzxmlDecomposerExe + " " + mzxmlFile + " " + nrOfDaughters + " " + outputDirectory;
stdout = stdout + "running " + fullcommand + "\n";		
exec(fullcommand);

class FileExtFilter implements FileFilter {
public FileExtFilter(String ext) {
this.ext = ext;
}
public boolean accept(File file) {
return file.getName().endsWith(ext);
}
String ext = null;
}

File dirObj = new File(outputDirectory);
String extension = "mzxml";
File[] fileObjList = dirObj.listFiles(new FileExtFilter(extension));
List filelist = new ArrayList();
for (int i = 0; i < fileObjList.length; i++) {
	filelist.add(fileObjList[i].getAbsolutePath());
}
String extension1 = "zip";
File[] fileObjList1 = dirObj.listFiles(new FileExtFilter(extension1));
List filelist1 = new ArrayList();
for (int i = 0; i < fileObjList1.length; i++) {
	fileObjList1[i].delete();
}

Script

// This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA). 
// Copyright© 2012 Yassene Mohammed
// Please send your feedback, questions, comments and suggestions for improvement to y.mohammed@lumc.nl
// 25 June 2012
// Yassene

String nrOfDaughters = nrOfDaughters;
String mzxmlFile = mzxmlFile;
String mzxmlDecomposerExe = mzxmlDecomposerExe;
//File fastaFileZipped = new File(fastaFileZipped);
File tandemExe = new File(tandemExe);
File runTandemExe = new File(runTandemExe);
String outputDirectory = mzxmlFile+"_xtandemResults";
String pepxmlComposerExe = pepxmlComposerExe;
File tandem2xmlExe = new File(tandem2xmlExe);

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Script

String fullcommand =indexmzXML + " " + mzxmlFile ;

stdout = stdout + "running " + fullcommand + "\n";		
exec(fullcommand);
File file1=new File(mzxmlFile);
File file3 = new File(mzxmlFile+".new");

        if(file3.exists()){
            boolean success= file1.delete();
        }
File file2=new File(mzxmlFile);
 file3.renameTo(file2);
File file = new File(mzxmlFile); 

String zipCommand = "zip -j "+ mzxmlFile+".zip "+file.getAbsolutePath();
exec(zipCommand);
stdout = stdout + zipCommand;

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