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<div class="title">FileMerger </div> </div>
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<div class="textblock"><p>Merges several files. Multiple output format supported, depending on input format.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> FileMerger <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1">any tool/instrument producing merge able files </td><td valign="middle" align="center" rowspan="1">any tool operating merged files (e.g. <a class="el" href="TOPP_XTandemAdapter.html">XTandemAdapter</a>) </td></tr>
</table>
</center><p>The meta information that is valid for the whole experiment (e.g. MS instrument and sample) is taken from the first file.</p>
<p>The retention times for the individual scans are taken from either: </p>
<ul>
<li>
the input file meta data (e.g. mzML) </li>
<li>
from the input file names (name must contain 'rt' directly followed by a number, e.g. 'myscan_rt3892.98_MS2.dta') </li>
<li>
as a list (one RT for each file) </li>
<li>
or are auto-generated (starting at 1 with 1 second increment). </li>
</ul>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
FileMerger -- Merges several MS files into one file.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
FileMerger <options>
Options (mandatory options marked with '*'):
-in <files>* Input files separated by blank (valid formats: 'mzData', 'mzXML', 'mzML', 'dta',
'dta2d', 'mgf', 'featureXML', 'consensusXML', 'fid', 'traML')
-in_type <type> Input file type (default: determined from file extension or content) (valid: 'mzDat
a', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'fid',
'traML')
-out <file>* Output file (valid formats: 'mzML', 'featureXML', 'consensusXML', 'traML')
-annotate_file_origin Store the original filename in each feature using meta value "file_origin" (for
featureXML and consensusXML only).
Flags for non-featureXML input/output:
-raw:rt_auto Assign retention times automatically (integers starting at 1)
-raw:rt_custom <rt> List of custom retention times that are assigned to the files. The number of given
retention times must be equal to the number of given input file.
-raw:rt_filename If this flag is set FileMerger tries to guess the rt of the file name.
This option is useful for merging DTA file, which should contain the string
'rt' directly followed by a floating point number:
i.e. my_spectrum_rt2795.15.dta
-raw:ms_level <num> This option is useful for use with DTA files which does not contain MS level inform
ation. The given level is assigned to the spectra. (default: '2')
-raw:user_ms_level If this flag is set, the MS level given above is used
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+FileMerger</span><span class="node_description">Merges several MS files into one file.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'FileMerger'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value">[]</span>
<span class="item_description">Input files separated by blank</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.fid,*.traML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">in_type</span><span class="item_value"></span>
<span class="item_description">Input file type (default: determined from file extension or content)</span><span class="item_tags"></span><span class="item_restrictions">mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,fid,traML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Output file</span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML,*.featureXML,*.consensusXML,*.traML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">annotate_file_origin</span><span class="item_value">false</span>
<span class="item_description">Store the original filename in each feature using meta value "file_origin" (for featureXML and consensusXML only).</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">+++raw</span><span class="node_description">Flags for non-featureXML input/output</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">rt_auto</span><span class="item_value">false</span>
<span class="item_description">Assign retention times automatically (integers starting at 1)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">rt_custom</span><span class="item_value">[]</span>
<span class="item_description">List of custom retention times that are assigned to the files. The number of given retention times must be equal to the number of given input file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">rt_filename</span><span class="item_value">false</span>
<span class="item_description">If this flag is set FileMerger tries to guess the rt of the file name.<br>This option is useful for merging DTA file, which should contain the string<br>'rt' directly followed by a floating point number:<br>i.e. my_spectrum_rt2795.15.dta</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">ms_level</span><span class="item_value">2</span>
<span class="item_description">This option is useful for use with DTA files which does not contain MS level information. The given level is assigned to the spectra.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">user_ms_level</span><span class="item_value">false</span>
<span class="item_description">If this flag is set, the MS level given above is used</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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