.TH "			\fBtandemwrapper\fP 		" "1" 
.SH "NAME" 
\fBtandemwrapper\fP 		 \(em 			run X!Tandem given its parameter file and path to X!Tandem software 
 
.SH "SYNOPSIS" 
.PP 
\fBtandemwrapper\fR [\fB\fIoptions\fR\fP]  [\fB\fIfilename ...\fR\fP]  
.SH "DESCRIPTION" 
.PP 
This manual page documents briefly the \fBtandemwrapper\fR software.  
 
This program can be used to run X!Tandem on data from Bruker's timsTOF line of  
instruments. It can also run X!Tandem on modern mzML files (any kind of compression type) 
 
 
.SH "OPTIONS" 
.IP "\fB-h | \-\-help\fP" 10 
Displays detailed usage information and exits. 
 
.IP "\fB-v | \-\-version\fP" 10 
Print the version of the software program. 
 
.IP "\fB\-\-tandem\fP" 10 
Full path to the X!Tandem executable file (tandem or 
tandem.exe). 
 
.IP "\fB-t | \-\-tmp\fP" 10 
Optionally set the temporary directory to store temporary 
data. 
 
.IP "\fIfilename\fR" 10 
X!Tandem parameter file (see the X!Tandem documentation on https://www.thegpm.org/TANDEM/. 
 
.SH "Bibliographic reference to be cited" 
.PP 
Langella O, Valot B, Balliau T, Blein-Nicolas M, Bonhomme L, Zivy M. (2017) X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. J. Proteome Res., 2 (16) 494-503  
 
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