de Bruin et al. Workflow 4
Created: 2012-08-01 09:08:13
Last updated: 2012-08-01 09:08:58
This is "Workflow 4" from de Bruin et al., Mol. Cell. Proteomics 2012.
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Workflow Components
Authors (0)
Titles (0)
Descriptions (0)
Dependencies (0)
Inputs (11)
Name |
Description |
msHybrid_Pars |
|
FTICR_Data_Dir |
|
pepAlign_Pars |
|
Result_Dir |
|
IT_Data_Dirs |
|
Log_File |
|
Tandem_Param_File |
|
FASTA_File |
|
Prophet_Pars |
|
msRecal_Pars |
|
Iterations |
|
Processors (6)
Name |
Type |
Description |
Workflow_3 |
workflow |
|
CompassXport |
workflow |
|
Mode_value |
stringconstant |
Value0 |
Multi_CompassXport |
workflow |
|
List_Data_Dirs |
localworker |
Script/****************** Input descriptions ****************/
// input port: String directory (depth 0)
// input port: String extension (depth 0)
// output port: String filelist (depth 0)
/****************** Class Declarations ****************/
class FileExtFilter implements FileFilter {
public FileExtFilter(String ext) {
this.ext = ext;
}
public boolean accept(File file) {
return (file.getName().endsWith(ext) && file.isDirectory());
}
String ext = null;
}// class
/************** Main matter, input checking ************/
if (extension == void || extension.equals("")) {
throw new RuntimeException("The 'extension' parameter cannot be null.");
}// if
if (directory == void || directory.equals("")) {
throw new RuntimeException("The 'directory' parameter cannot be null.");
}// if
File dirObj = new File(directory);
if (!dirObj.exists()) {
throw new RuntimeException(
"The 'directory' parameter specified does not exist.");
}// if
/************ Main matter, Running algorithm **********/
File[] fileObjList = dirObj.listFiles(new FileExtFilter(extension));
List filelist = new ArrayList();
for (int i = 0; i < fileObjList.length; i++) {
filelist.add(fileObjList[i].getAbsolutePath());
}
|
Dir_Ext |
stringconstant |
Value.d |
Beanshells (9)
Name |
Description |
Inputs |
Outputs |
Tandem |
|
mzxml_file
fasta_file
parameter_file
log_file
|
tandem_file
|
PeptideProphet |
|
input_files
arguments
log_file
|
output_file
|
CompassXport |
|
raw_data_dir
raw_flag
log_file
result_dir
|
output_file
|
CompassXport |
|
raw_data_dir
raw_flag
log_file
result_dir
|
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
|
msRecal |
|
mzXML_file
pepXML_files
arguments
log_file
|
mzXML_output
|
Loop_Decrementer |
|
in_num
|
out_num
|
Outputs (3)
Name |
Description |
Hybrid_IT_mzXML_Files |
|
Recal_FT_mzXML_File |
|
Final_count |
|
Datalinks (23)
Source |
Sink |
msRecal_Pars |
Workflow_3:msRecal_Pars |
Prophet_Pars |
Workflow_3:Prophet_Pars |
Tandem_Param_File |
Workflow_3:Tandem_Param_File |
Log_File |
Workflow_3:Log_File |
FASTA_File |
Workflow_3:FASTA_File |
pepAlign_Pars |
Workflow_3:pepAlign_Pars |
msHybrid_Pars |
Workflow_3:msHybrid_Pars |
Iterations |
Workflow_3:Loop_cnt |
CompassXport:mzXML_Output |
Workflow_3:FT_mzXML_File |
Multi_CompassXport:mzXML_Output |
Workflow_3:IT_mzXML_Files |
FTICR_Data_Dir |
CompassXport:Raw_Data_Dir |
Log_File |
CompassXport:Log_File |
Result_Dir |
CompassXport:Result_Dir |
Mode_value:value |
CompassXport:Mode |
Mode_value:value |
Multi_CompassXport:Mode |
Result_Dir |
Multi_CompassXport:Result_Dir |
Log_File |
Multi_CompassXport:Log_File |
List_Data_Dirs:filelist |
Multi_CompassXport:Raw_Data_Dir |
IT_Data_Dirs |
List_Data_Dirs:directory |
Dir_Ext:value |
List_Data_Dirs:extension |
Workflow_3:IT_mzXML_Files |
Hybrid_IT_mzXML_Files |
Workflow_3:FT_mzXML_File |
Recal_FT_mzXML_File |
Workflow_3:Loop_cnt |
Final_count |
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License
All versions of this Workflow are
licensed under:
Version 1
(of 1)
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