tries to launch condor jobs with the number of cpus requested in X!Tandem model

src/fr/inra/pappso/xtandempipeline/thread/XtandemCondorAnalysis.java

@@ -41,12 +41,8 @@ public class XtandemCondorAnalysis extends xtandem_analysis {
 		logger.info("Corrected xtandem preset error");
 		xtandem_params params = new xtandem_params();
 		params.load_xml(model);
-		xtandem_param paramThreads = params.get_param_to("spectrum, threads");
-		//don't use threads in condor analysis
-		paramThreads.setValue("1");
-		params.save_to_xml(model);
 
-		File condorSubmitFile = newCondorSubmitFile();
+		File condorSubmitFile = newCondorSubmitFile(params);
 
 		base_shell pipe = new base_shell();
 		pipe.set_commande(new String[] {
@@ -72,7 +68,16 @@ public class XtandemCondorAnalysis extends xtandem_analysis {
 
 	}
 
-	private File newCondorSubmitFile() throws MSMSException {
+	private File newCondorSubmitFile(xtandem_params params)
+			throws MSMSException {
+		xtandem_param paramThreads = params.get_param_to("spectrum, threads");
+		int requestedCpus = 0;
+		if (paramThreads != null) {
+			// get requested number of cpus from model :
+			requestedCpus = Integer.valueOf(paramThreads.getValue());
+
+		}
+
 		createTempDirectoryForCondor();
 		XtandemDatabaseXmlFile databasexml = new XtandemDatabaseXmlFile(tmpDir,
 				databases);
@@ -88,14 +93,6 @@ public class XtandemCondorAnalysis extends xtandem_analysis {
 		XtandemModelFile modelTmp = new XtandemModelFile(new File(
 				tmpDir.getAbsolutePath() + System.getProperty("file.separator")
 						+ model.getName()));
-		try {
-			xtandem_params params = new xtandem_params();
-			params.load_xml(model);
-			params.get_param_to("spectrum, threads").setValue("1");
-			params.save_to_xml(modelTmp);
-		} catch (Exception e) {
-			throw new MSMSException("Unable to copy model\n" + e.getMessage());
-		}
 
 		/*
 		 * copy database.xml xtandem_param3542072178348339854.xml
@@ -107,6 +104,10 @@ public class XtandemCondorAnalysis extends xtandem_analysis {
 		out.open(condorSubmitTxtFile.getAbsolutePath());
 		out.write("Universe   = vanilla" + "\n");
 		out.write("Rank       = Mips" + "\n");
+		if ((requestedCpus > 0) && (requestedCpus < 200)) {
+			out.write("request_cpus = " + requestedCpus + "\n");
+		}
+
 		out.write("Executable = " + conf.getXtandem_link().getAbsolutePath()
 				+ "\n");
 		out.write("Log        = " + condorTandemLogFile.getAbsolutePath()