idconvert1

Usage

Overview

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.