
#include	/jump/to/other/settingfile.txt

#No	Home Dir	Main File	MS2 File	Conf Dir	AdductIon File	IonizationMode File	MFSearcher File	Annotation File	Parameter File	AdductUnitFile	RepeatUnitFile	Output Dir	Copy MS Files	Make Analysis Dir	Analysis Name	ExtraFile1
1	C:\your\dir\home	Sample1_ms1.txt		C:\your\dir\conf	adductIon_pos.txt	ionizationMode_pos.txt	mfsearcher.txt	annotation.txt	parameters.txt	adductUnit_pos.txt	repeatUnit_pos.txt	C:\your\dir\outbase\Sample1_ms1	TRUE	TRUE	Sample1_ms1	C:\your\dir\extra\file1
2	C:\your\dir\home	Sample2.mzXML		C:\your\dir\conf	adductIon_pos.txt	ionizationMode_pos.txt	mfsearcher.txt	annotation.txt	parameters.txt	adductUnit_pos.txt	repeatUnit_pos.txt	C:\your\dir\outbase\Sample2	TRUE	TRUE	Sample2	C:\your\dir\extra\file2
#3	C:\your\dir\home	Sample3.mzXML		C:\your\dir\conf	adductIon_pos.txt	ionizationMode_pos.txt	mfsearcher.txt	annotation.txt	parameters.txt	adductUnit_pos.txt	repeatUnit_pos.txt	C:\your\dir\outbase\Sample3	TRUE	TRUE	Sample3	C:\your\dir\extra\file3


#exit   // for quit here
skip   // for skip to "resume" label
resume // for resume process

mode_seq // enter to sequencial setting mode
         // only for the mzXML or mzML files.

homeDir	/path/to/dir/home
confDir	/path/to/dir/conf
outDirBase	/path/to/dir/out
#adductIon	adductIon.txt // name of adductIon file in the conf director
#ionizationMode	ionizationMode.txt
#mfsearcher	mfsearcher.txt
#annotation	annotation.txt
#adductUnit	adductUnit.txt
#repeatUnit	repeatUnit.txt
#copyMsFiles	true // ture | false
#makeAnalysisDir	true // true | false
#extraFile	/path/to/extraFile.txt

parameter	param_m1.txt
#parameterSub	b	param_m1b.txt
#parameterSub	c	param_m1c.txt

1	SampleFile1  // without file extension
2	SampleFile2  // without file extension

#3	SampleFile1	b
#4	SampleFile1	c


parameter	param_m1_mock.txt

5	MockFile1  // without file extension

homeDir	/path/to/other/dir/home
confDir	/path/to/other/dir/conf
outDirBase	/path/to/other/dir/out

6	MockFile2  // without file extension

mode_list // enter to list setting mode (default)

#4	C:\your\dir\home	Sample4.mzXML		C:\your\dir\conf	adductIon_pos.txt	ionizationMode_pos.txt	mfsearcher.txt	annotation.txt	parameters.txt	adductUnit_pos.txt	repeatUnit_pos.txt	C:\your\dir\outbase\Sample4	TRUE	TRUE	Sample4	C:\your\dir\extra\file3


exit