jmzTab Utilities

Introduction

We create two interfaces, CLI (mzTabCLI) and Simple GUI (mzTabGUI), to simplify the usage of jmzTab APIs. Compared with GUI, command line provides more flexible way to batch process the mzTab files.

Command Line Interface

In mzTabCLI Demo, we provide a couple of examples to help user call command line interface quickly.

• print command line help

java -jar mzTabCLI.jar -help

The output will like following:

usage: jmztab
 -check inFile=<inFile>                     Choose a file from input directory. This
                                            parameter should not be null!
 -convert inFile=<inFile> format=<format>   Converts the given format file (PRIDE or MZIDENTML) to an mztab
                                            file.
 -h,--help                                  print help message
 -message code=<code>                       print Error/Warn detail message based on code
                                            number.
 -outFile <arg>                             Dump output data to the given file. If
                                            not set, output data will be dumped on stdout.

• print special error/warn message based on code, see details of Error/Warn Message List.

java -jar mzTabCLI.jar -message code=2000

The output would be like:

    Code:       2000
Category:       Logical
Original:       Column "{0}" is an empty cell, or the current column cannot use "null".
   Cause:       In the table-based sections (protein, peptide, psm, and small molecule) there MUST NOT be any empty cells. Missing values MUST be reported using "null".

1. **Code:** Unique number for error/warn
1. **Category:** Currently, there are three types of messages: _**Format, Logical**_
1. **Original:** Message expression pattern. "{?}" is a couple of parameters which can be filled during validate processing.
1. **Cause:** A readable text to describe the reason why raise this error/warn. Currently, these cause message coming from mztab specification mainly.

• Exists warn/error messages during validate, print messages on screen:

java -Xms2048m -jar mzTabCLI.jar -check inFile=temp/SILAC_CQI.mzTab

The output would be like:

Begin check mztab file: c:\work\jmztab2\target\jmztab\testset\mztab_merged_example.txt
[Warn-2018] line 13: Software parameter "[MS, MS:1001583, MaxQuant,]" does not contain version information.
[Warn-2001] line 36: Column "search_engine_score_ms_run[6]" field value does not allow a "null" value.
Finish!

• Exists warn/error messages during validate, print messages into SILAC_CQI.err file:

java -Xms2048m -jar mzTabCLI.jar -check inFile=temp/SILAC_CQI.mzTab -outFile SILAC_CQI.err

• Convert PRIDE_Exp_Complete_Ac_16649.xml, and print mzTab file to screen:

java -Xms2048m -jar mzTabCLI.jar -convert inFile=temp/PRIDE_Exp_Complete_Ac_16649.xml format=PRIDE

• Convert PRIDE_Exp_Complete_Ac_16649.xml, and print mzTab file to PRIDE_Exp_Complete_Ac_16649.mztab:

java -Xms2048m -jar mzTabCLI.jar -convert inFile=temp/PRIDE_Exp_Complete_Ac_16649.xml format=PRIDE -outFile PRIDE_Exp_Complete_Ac_16649.mztab

---

Simple GUI

There are some screenshots about how to use GUI (Click on a screenshot to see the full size version):