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<div class="title">FileConverter </div> </div>
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<div class="textblock"><p>Converts between different MS file formats.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> FileConverter <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_GenericWrapper.html">GenericWrapper</a> (e.g. for calling external converters) </td><td valign="middle" align="center" rowspan="2">any tool operating on the output format </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1">any vendor software exporting supported formats (e.g. mzXML) </td></tr>
</table>
</center><p>The main use of this tool is to convert data from external sources to the formats used by OpenMS/TOPP. Maybe most importantly, data from MS experiments in a number of different formats can be converted to mzML, the canonical file format used by OpenMS/TOPP for experimental data. (mzML is the PSI approved format and supports traceability of analysis steps.)</p>
<p>Many different format conversions are supported, and some may be more useful than others. Depending on the file formats involved, information can be lost during conversion, e.g. when converting featureXML to mzData. In such cases a warning is shown.</p>
<p>The input and output file types are determined from the file extensions or from the first few lines of the files. If file type determination is not possible, the input or output file type has to be given explicitly.</p>
<p>Conversion with the same output as input format is supported. In some cases, this can be helpful to remove errors from files, to update file formats to new versions, or to check whether information is lost upon reading or writing.</p>
<p>Some information about the supported input types: <a class="el" href="classOpenMS_1_1MzMLFile.html">mzML</a> <a class="el" href="classOpenMS_1_1MzXMLFile.html">mzXML</a> <a class="el" href="classOpenMS_1_1MzDataFile.html">mzData</a> <a class="el" href="classOpenMS_1_1MascotGenericFile.html">mgf</a> <a class="el" href="classOpenMS_1_1DTA2DFile.html">dta2d</a> <a class="el" href="classOpenMS_1_1DTAFile.html">dta</a> <a class="el" href="classOpenMS_1_1FeatureXMLFile.html">featureXML</a> <a class="el" href="classOpenMS_1_1ConsensusXMLFile.html">consensusXML</a> <a class="el" href="classOpenMS_1_1MS2File.html">ms2</a> <a class="el" href="classOpenMS_1_1XMassFile.html">fid/XMASS</a> <a class="el" href="classOpenMS_1_1MsInspectFile.html">tsv</a> <a class="el" href="classOpenMS_1_1SpecArrayFile.html">peplist</a> <a class="el" href="classOpenMS_1_1KroenikFile.html">kroenik</a> <a class="el" href="classOpenMS_1_1EDTAFile.html">edta</a></p>
<p>See <a class="el" href="TOPP_IDFileConverter.html">IDFileConverter</a> for similar functionality for protein/peptide identification file formats.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
FileConverter -- Converts between different MS file formats.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
FileConverter <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'mzData', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXM
L', 'consensusXML', 'ms2', 'fid', 'tsv', 'peplist', 'kroenik', 'edta')
-in_type <type> Input file type -- default: determined from file extension or content
(valid: 'mzData', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML'
, 'ms2', 'fid', 'tsv', 'peplist', 'kroenik', 'edta')
-out <file>* Output file (valid formats: 'mzData', 'mzXML', 'mzML', 'dta2d', 'mgf', 'featureXML',
'consensusXML', 'edta')
-out_type <type> Output file type -- default: determined from file extension or content
(valid: 'mzData', 'mzXML', 'mzML', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'edta
')
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">+FileConverter</span><span class="node_description">Converts between different MS file formats.</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 'FileConverter'</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 file </span><span class="item_tags">input file</span><span class="item_restrictions">*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.ms2,*.fid,*.tsv,*.peplist,*.kroenik,*.edta</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<br></span><span class="item_tags"></span><span class="item_restrictions">mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,ms2,fid,tsv,peplist,kroenik,edta</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">*.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out_type</span><span class="item_value"></span>
<span class="item_description">output file type -- default: determined from file extension or content<br></span><span class="item_tags"></span><span class="item_restrictions">mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">TIC_DTA2D</span><span class="item_value">false</span>
<span class="item_description">Export the TIC instead of the entire experiment in mzML/mzData/mzXML -> DTA2D conversions.</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>
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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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