.TH "      \fBIDCONVERT\fP     " "1" 
.SH "NAME" 
\fBidconvert\fP      \(em       Convert mass spectrometry identification file formats. 
 
.SH "SYNOPSIS" 
.PP 
\fBidconvert\fR [\fB\fIoptions\fR\fP]  [\fB\fIfilemasks\fR\fP]  
.SH "DESCRIPTION" 
.PP 
This manual page documents briefly 
the \fBidconvert\fR software shipped within the 
\fBlibpwiz-tools\fP package. This program allows 
one to convert mass spectrometry protein identification data 
files from one format to another. 
 
.SH "OPTIONS" 
.IP "\-v | \-\-verbose" 10 
Display detailed processing progress information. 
 
.IP "\-f | \-\-filelist \fIfilename\fR" 10 
Uses the contents of \fIfilename\fR which lists filenames. 
 
.IP "\-o | \-\-outdir \fIdir\fR" 10 
Set the output directory ('\-' for stdout) to \fIdir\fR. By default, the output directory is '.' (that is, the current working directory). 
 
.IP "\-c | \-\-config \fIfilename\fR" 10 
Set the configuration file to \fIfilename\fR. 
 
.IP "\-e | \-\-ext \fIext\fR" 10 
Set the extension of the output files 
to \fIext\fR. Can 
be mzid or pepXML or txt. 
 
.IP "\-\-mzIdentML" 10 
Write \fBmzIdentML\fP format (default). 
 
.IP "\-\-pepXML" 10 
Write \fBpepXML\fP format. 
 
.IP "\-\-text" 10 
Write hierarchical \fBtext\fP format. 
 
.SH "EXAMPLES" 
.PP 
Convert sequest.pepXML to sequest.mzid 
 
.PP 
\fBidconvert sequest.pepXML\fR      
.PP 
Convert mascot.mzid to mascot.pepXML 
 
.PP 
\fBidconvert mascot.mzid \-\-pepXML\fR      
.PP 
Use a configuration file 
 
.PP 
\fBidconvert xtandem.pep.xml \-c config.txt\fR      
.SH "RETURN VALUE" 
.PP 
The number of failed files. 
 
.SH "AUTHOR" 
.PP 
Filippo Rusconi <lopippo@debian.org>  
.PP 
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. 
 
.PP 
On a Debian system the complete text of the GNU General 
Public License version 3 can be found in the file 
`\fB/usr/share/common-licenses/GPL\-3\fP'. 
 
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