idconvert.1

       Filippo Rusconi <lopippo@debian.org>

       This  manual page was written by Filippo Rusconi <lopippo@debian.org> (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'.

                                                                                               IDCONVERT     (1)

       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.

       Convert sequest.pepXML to sequest.mzid

       idconvertsequest.pepXML

       Convert mascot.mzid to mascot.pepXML

       idconvertmascot.mzid--pepXML

       Use a configuration file

       idconvertxtandem.pep.xml-cconfig.txt

idconvert      —       Convert mass spectrometry identification file formats.

       -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.

       The number of failed files.

idconvert [options][filemasks]