de Bruin et al. Workflow 3

None

/****************** Input descriptions ****************/
// input port: String mzXML_file (depth 0)
// input port: String pepXML_files (depth 1)
// input port: String log_file (depth 0)
// input port: String arguments (depth 0)
// output port: String mzXML_output (depth 0)


/****************** Class Declarations ****************/
class InProcStreamReader extends Thread
{
    private StringBuffer sb;
    public  InputStream is;
    
    InProcStreamReader(InputStream is) {
        this.is = is;
    }// InProcStreamReader(InputStream is) 
    
    public void run() {
        try {
            InputStreamReader isr = new InputStreamReader(is);
            sb = new StringBuffer();
            while ((c = isr.read()) != -1)
                sb.append((char) c);
        } catch (IOException ioe)
        {
          ioe.printStackTrace();  
        }/// catch
    }// run

    public String getOutput() { 
      return sb.toString();
    }// getOutput
}// InProcStreamReader


/****************** Global variables ******************/
// Global variable for tools path
installDir = "C:\\Users\\nmpalmblad\\MCP_Workflows\\MCP_Workflows\\";


/****************** Global functions ******************/
// Generates the output file name based on the input directory
String genOutputFileName(String inputFile) {
  int dotPos = inputFile.lastIndexOf(".");
  return (inputFile.substring(0, dotPos) + "_RC.mzXML");
}// String genOutputFileName(String inputFile) 


/************** Main matter, input checking ************/
// Checking the input directory
if (mzXML_file == void || mzXML_file.equals("")) {
  throw new RuntimeException("The 'mzXML_file' port cannot be null or empty.");
} else if (pepXML_files == void || pepXML_files.size() == 0) {
  throw new RuntimeException("The 'pepXML_files' port cannot be null or empty.");
}

/************ Main matter, Running executable **********/
// Setting up the command line 
appArray = new ArrayList();

// Adding the command itself
appArray.add(installDir + "Tools\\msRecal\\msRecal.exe");

// Adding the input arguments
appArray.add("-m" + mzXML_file);

for(i=0; i

Name	Description
FT_mzXML_File
Tandem_Param_File
FASTA_File
IT_mzXML_Files
Prophet_Pars
Log_File
pepAlign_Pars
msHybrid_Pars
msRecal_Pars
Loop_cnt

Name	Type	Description
Workflow_2	workflow
msRecal	beanshell	Script /**************** Input descriptions ************/ // input port: String mzXML_file (depth 0) // input port: String pepXML_files (depth 1) // input port: String log_file (depth 0) // input port: String arguments (depth 0) // output port: String mzXML_output (depth 0) /************** Class Declarations ************/ class InProcStreamReader extends Thread { private StringBuffer sb; public InputStream is; InProcStreamReader(InputStream is) { this.is = is; }// InProcStreamReader(InputStream is) public void run() { try { InputStreamReader isr = new InputStreamReader(is); sb = new StringBuffer(); while ((c = isr.read()) != -1) sb.append((char) c); } catch (IOException ioe) { ioe.printStackTrace(); }/// catch }// run public String getOutput() { return sb.toString(); }// getOutput }// InProcStreamReader /************** Global variables **************/ // Global variable for tools path installDir = "C:\\Users\\nmpalmblad\\MCP_Workflows\\MCP_Workflows\\"; /************** Global functions **************/ // Generates the output file name based on the input directory String genOutputFileName(String inputFile) { int dotPos = inputFile.lastIndexOf("."); return (inputFile.substring(0, dotPos) + "_RC.mzXML"); }// String genOutputFileName(String inputFile) /********** Main matter, input checking ********/ // Checking the input directory if (mzXML_file == void \|\| mzXML_file.equals("")) { throw new RuntimeException("The 'mzXML_file' port cannot be null or empty."); } else if (pepXML_files == void \|\| pepXML_files.size() == 0) { throw new RuntimeException("The 'pepXML_files' port cannot be null or empty."); } /******** Main matter, Running executable ********/ // Setting up the command line appArray = new ArrayList(); // Adding the command itself appArray.add(installDir + "Tools\\msRecal\\msRecal.exe"); // Adding the input arguments appArray.add("-m" + mzXML_file); for(i=0; i
Loop_Decrementer	beanshell	Script // decreases loop val +1 // input_port: in_num // output_port: out_num aInt = Integer.parseInt(in_num); aInt--; out_num = aInt.toString();
Echo_List	localworker	Script outputlist = inputlist;

Name	Inputs	Outputs
msRecal	mzXML_file pepXML_files arguments log_file	mzXML_output
Loop_Decrementer	in_num	out_num
PeptideProphet	input_files arguments log_file	output_file
pepAlign	mzXML_file pepXML_file arguments log_file	plf_output
pepWarp	mzXML_file pepXML_file plf_file log_file	pepXML_output
msHybrid	IT_mzXML_file FT_mzXML_file plf_file log_file arguments	mzXML_output
Tandem	mzxml_file fasta_file parameter_file log_file	tandem_file

Name	Description
IT_mzXML_Files
FT_mzXML_File
Loop_cnt

Source	Sink
FT_mzXML_File	Workflow_2:FT_mzXML_File
Tandem_Param_File	Workflow_2:Tandem_Param_File
FASTA_File	Workflow_2:FASTA_File
Prophet_Pars	Workflow_2:Prophet_Pars
Log_File	Workflow_2:Log_File
pepAlign_Pars	Workflow_2:pepAlign_Pars
msHybrid_Pars	Workflow_2:msHybrid_Pars
IT_mzXML_Files	Workflow_2:IT_mzXML_File
msRecal_Pars	msRecal:arguments
Log_File	msRecal:log_file
Workflow_2:Warped_pepXML_File	msRecal:pepXML_files
FT_mzXML_File	msRecal:mzXML_file
Loop_cnt	Loop_Decrementer:in_num
Workflow_2:Hybrid_IT_mzXML_File	Echo_List:inputlist
Echo_List:outputlist	IT_mzXML_Files
msRecal:mzXML_output	FT_mzXML_File
Loop_Decrementer:out_num	Loop_cnt

de Bruin et al. Workflow 3

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