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<div class="textblock"><p>Shows basic information about the data in an <a class="el" href="namespaceOpenMS.html" title="Main OpenMS namespace. ">OpenMS</a> readable file.</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 $" src="form_91.png"/> FileInfo <img class="formulaInl" alt="$ \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 operating on MS peak data <br/>
(in mzML format) </td><td valign="middle" align="center" rowspan="1">none ; console or text file </td></tr>
</table>
</center><p>This tool can show basic information about the data in several peak, feature and consensus feature files. It can</p>
<ul>
<li>show information about the data range of a file (m/z, RT, intensity)</li>
<li>show a statistical summary for intensities, qualities, feature widths</li>
<li>show an overview of the metadata</li>
<li>validate several XML formats against their XML schema</li>
<li>check for corrupt data in a file (e.g., duplicate spectra)</li>
</ul>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
FileInfo -- Shows basic information about the file, such as data ranges and file type.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
FileInfo <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'mzData', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXM
L', 'consensusXML', 'idXML', 'pepXML', 'fid')
-in_type <type> Input file type -- default: determined from file extension or content (valid: 'mzData',
'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'idXML', 'pepXML',
'fid')
-out <file> Optional output file. If left out, the output is written to the command line. (valid
formats: 'txt')
-m Show meta information about the whole experiment
-p Shows data processing information
-s Computes a five-number statistics of intensities, qualities, and widths
-d Show detailed listing of all spectra and chromatograms (peak files only)
-c Check for corrupt data in the file (peak files only)
-v Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML
)
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">+FileInfo</span><span class="node_description">Shows basic information about the file, such as data ranges and file type.</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 'FileInfo'</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,*.idXML,*.pepXML,*.fid</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,idXML,pepXML,fid</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Optional output file. If left out, the output is written to the command line.</span><span class="item_tags">output file</span><span class="item_restrictions">*.txt</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">out_tsv</span><span class="item_value"></span>
<span class="item_description">Second optional output file. Tab separated flat text file.</span><span class="item_tags">output file</span><span class="item_restrictions">*.csv</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">m</span><span class="item_value">false</span>
<span class="item_description">Show meta information about the whole experiment</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">p</span><span class="item_value">false</span>
<span class="item_description">Shows data processing information</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">s</span><span class="item_value">false</span>
<span class="item_description">Computes a five-number statistics of intensities, qualities, and widths</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">d</span><span class="item_value">false</span>
<span class="item_description">Show detailed listing of all spectra and chromatograms (peak files only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">c</span><span class="item_value">false</span>
<span class="item_description">Check for corrupt data in the file (peak files only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">v</span><span class="item_value">false</span>
<span class="item_description">Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)</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>
<p>In order to enrich the resulting data of your anaysis pipeline or to quickly compare different outcomes of your pipeline you can invoke the aforementioned information of your input data and (intermediary) results. </p>
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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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