SYNOPSIS

idconvert [options] [filemasks]

DESCRIPTION

This manual page documents briefly the idconvert software shipped within the libpwiz-tools package. This program allows one to convert mass spectrometry protein identification data files from one format to another.
 

OPTIONS

-v | --verbose

Display detailed processing progress information.
 

-f | --filelist filename

Uses the contents of filename which lists filenames.
 

-o | --outdir dir

Set the output directory ('-' for stdout) to dir. By default, the output directory is '.' (that is, the current working directory).
 

-c | --config filename

Set the configuration file to filename.
 

-e | --ext ext

Set the extension of the output files to ext. Can be mzid or pepXML or txt.
 

--mzIdentML

Write mzIdentML format (default).
 

--pepXML

Write pepXML format.
 

--text

Write hierarchical text format.
 

EXAMPLES

Convert sequest.pepXML to sequest.mzid
 

idconvert sequest.pepXML

Convert mascot.mzid to mascot.pepXML
 

idconvert mascot.mzid --pepXML

Use a configuration file
 

idconvert xtandem.pep.xml -c config.txt

RETURN VALUE

The number of failed files.
 

AUTHOR

Filippo Rusconi <[email protected]>

This manual page was written by Filippo Rusconi <[email protected]> (initial writing 05 december 2013). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3, published by the Free Software Foundation.
 

On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL-3'.