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<div class="title">SpectraMerger </div> </div>
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<div class="textblock"><p>Allows to add up several spectra.</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 $" src="form_91.png"/> SpectraMerger <img class="formulaInl" alt="$ \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">any tool operating on MS peak data <br/>
(in mzML format) </td></tr>
</table>
</center><dl class="experimental"><dt><b><a class="el" href="experimental.html#_experimental000024">Experimental classes:</a></b></dt><dd>This TOPP-tool is not well tested and not all features might be properly implemented and tested!</dd></dl>
<p>This tool can add several consecutive scans, increasing S/N ratio (for MS1 and above) or merge scans which stem from similar precursors (for MS2 and above).</p>
<p>In any case, the number of scans will be reduced.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
SpectraMerger -- Merges spectra (each MS level separately), increasing S/N ratios.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
SpectraMerger <options>
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.
Options (mandatory options marked with '*'):
-in <file>* Input mzML file. (valid formats: 'mzML')
-out <file>* Output mzML file with merged spectra. (valid formats: 'mzML')
-merging_method <method> Method of merging which should be used. (default: 'block_method' valid: 'precurso
r_method', 'block_method')
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)
The following configuration subsections are valid:
- algorithm Algorithm section for merging spectra
You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.
</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">+SpectraMerger</span><span class="node_description">Merges spectra (each MS level separately), increasing S/N ratios.</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 'SpectraMerger'</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 mzML file.</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML</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 mzML file with merged spectra.</span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">merging_method</span><span class="item_value">block_method</span>
<span class="item_description">Method of merging which should be used.</span><span class="item_tags"></span><span class="item_restrictions">precursor_method,block_method</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">+++algorithm</span><span class="node_description">Algorithm section for merging spectra</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:32px;">mz_binning_width</span><span class="item_value">0.0001</span>
<span class="item_description">Max m/z distance of two peaks to be merged.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">mz_binning_width_unit</span><span class="item_value">Da</span>
<span class="item_description">Unit in which the distance between two peaks is given.</span><span class="item_tags"></span><span class="item_restrictions">Da,ppm</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">sort_blocks</span><span class="item_value">RT_ascending</span>
<span class="item_description">Sort blocks by <?> before merging them (useful for precursor order)</span><span class="item_tags"></span><span class="item_restrictions">RT_ascending, RT_descending</span></div> <div class="node"><span class="node_name">++++block_method</span><span class="node_description"></span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">ms_levels</span><span class="item_value">[1]</span>
<span class="item_description">Merge spectra of this level. All spectra with other MS levels remain untouched.</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">rt_block_size</span><span class="item_value">5</span>
<span class="item_description">Maximum number of scans to be summed up.</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">rt_max_length</span><span class="item_value">0</span>
<span class="item_description">Maximum RT size of the block in seconds (0.0 = no size restriction).</span><span class="item_tags"></span><span class="item_restrictions">0:100000000000</span></div> <div class="node"><span class="node_name">++++precursor_method</span><span class="node_description"></span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">mz_tolerance</span><span class="item_value">0.0001</span>
<span class="item_description">Max m/z distance of the precursor entries of two spectra to be merged in [Da].</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">rt_tolerance</span><span class="item_value">5</span>
<span class="item_description">Max RT distance of the precursor entries of two spectra to be merged in [s].</span><span class="item_tags"></span><span class="item_restrictions">0:∞</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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