From 7d77653ef60a74e6371c3c879fdbe91ef8cb86a5 Mon Sep 17 00:00:00 2001 From: alchemistmatt Date: Tue, 22 Jan 2019 11:29:25 -0800 Subject: [PATCH] Update syntax shown at the command line --- .../java/edu/ucsd/msjava/params/ParamManager.java | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/src/main/java/edu/ucsd/msjava/params/ParamManager.java b/src/main/java/edu/ucsd/msjava/params/ParamManager.java index 33ce628e..33446302 100644 --- a/src/main/java/edu/ucsd/msjava/params/ParamManager.java +++ b/src/main/java/edu/ucsd/msjava/params/ParamManager.java @@ -92,7 +92,12 @@ public void printUsageInfo() { System.out.println(example); System.out.println(); - System.out.println("Documentation: https://github.com/MSGFPlus/msgfplus"); + System.out.println(); + System.out.println("For Thermo .raw files, obtain a centroided .mzML file using MSConvert, which is part of ProteoWizard (http://proteowizard.sourceforge.net/)"); + System.out.println(" MSConvert.exe DatasetName.raw --filter \"peakPicking true 1-\" --mzML --32"); + System.out.println(); + System.out.println("Documentation: https://msgfplus.github.io/msgfplus/"); + System.out.println("Releases: https://github.com/MSGFPlus/msgfplus/releases"); } public void printValues() { @@ -150,6 +155,7 @@ public void addSpecFileParam() { specFileParam.addFileFormat(SpecFileFormat.DTA_TXT); specFileParam.addFileFormat(FileFormat.DIRECTORY); specFileParam.fileMustExist(); + specFileParam.setAdditionalDescription("Spectra should be centroided (see below for MSConvert example). Profile spectra will be ignored."); addParameter(specFileParam); } @@ -372,8 +378,8 @@ public void addMSGFPlusParams() { maxMissedCleavages.defaultValue(-1); addParameter(maxMissedCleavages); - addExample("Example (high-precision): java -Xmx3500M -jar MSGFPlus.jar -s test.mzML -d IPI_human_3.79.fasta -inst 1 -t 20ppm -ti -1,2 -ntt 2 -tda 1 -o testMSGFPlus.mzid"); - addExample("Example (low-precision): java -Xmx3500M -jar MSGFPlus.jar -s test.mzML -d IPI_human_3.79.fasta -inst 0 -t 0.5Da,2.5Da -ntt 2 -tda 1 -o testMSGFPlus.mzid"); + addExample("Example (high-precision): java -Xmx3500M -jar MSGFPlus.jar -s test.mzML -d IPI_human_3.79.fasta -inst 1 -t 20ppm -ti -1,2 -ntt 2 -tda 1 -o testMSGFPlus.mzid -mod Mods.txt"); + addExample("Example (low-precision): java -Xmx3500M -jar MSGFPlus.jar -s test.mzML -d IPI_human_3.79.fasta -inst 0 -t 0.5Da,2.5Da -ntt 2 -tda 1 -o testMSGFPlus.mzid -mod Mods.txt"); // Hidden parameters FileParameter dbIndexDirParam = new FileParameter("dd", "DBIndexDir", "Path to the directory containing database index files");