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<div class="title">PILISIdentification </div> </div>
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<div class="textblock"><p>Performs an ProteinIdentification with PILIS</p>
<dl class="experimental"><dt><b><a class="el" href="experimental.html#_experimental000015">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>
<center> <table class="doxtable">
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<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> PILISIdentification <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="2"><a class="el" href="TOPP_PILISModelTrainer.html">PILISModelTrainer</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_ConsensusID.html">ConsensusID</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDMapper.html">IDMapper</a> </td></tr>
</table>
</center><p>The PILISIdentification TOPP tool performs a ProteinIdentification run with the PILIS ProteinIdentification engine. As input the file given in the in parameters is used. The identifications are written into an idXML file given in the out parameter. Additionally the model_file must be specified. To perform a search also a peptide database file should be used,given in the peptide_db_file parameter. This should contain a peptide in a separate line, either only the sequence or additionally with weight and charge in the second and third column.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
PILISIdentification -- performs a peptide/protein identification with the PILIS engine
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
PILISIdentification <options>
Options (mandatory options marked with '*'):
-in <file>* Input file in MzML format (valid formats: 'mzML')
-out <file>* Output file in idXML format (valid formats: 'idXML')
-model_file <file* The model file of the PILISModel
-peptide_db_file <file>* A file which should contain peptides in the format
DFPIANGER 1019.09 1
where the first column is the peptide, the second the m
/z
the third the charge. As a alternative the sequence fil
e
may contain only peptide sequences each in a separate l
ine
repectively
-precursor_mass_tolerance <tol> The precursor mass tolerance (default: '2')
-peak_mass_tolerance <tol> The peak mass tolerance (default: '1')
-max_pre_candidates <int> Number of candidates that are used for precise scoring
(default: '200')
-max_candidates <int> Number of candidates that are reported by PILIS (default
: '20')
-upper_mz <double> Upper mz interval endpoint (default: '2000')
-lower_mz <double> Lower mz interval endpoint (default: '200')
-fixed_modifications <mods> Monoisotopic_mass@residues e.g.: 57.021464@C
Parameters of PILISModel:
-model:charge_directed_threshold <double> Bla (default: '0.3')
-model:charge_remote_threshold <double> Bla (default: '0.2')
-model:charge_loss_factor <double> Bla (default: '0.5')
-model:min_y_ion_intensity <double> (default: '0.2')
-model:min_b_ion_intensity <double> (default: '0.15')
-model:min_a_ion_intensity <double> (default: '0.05')
-model:min_y_loss_intensity <double> (default: '0.05')
-model:min_b_loss_intensity <double> (default: '0.02')
-model:visible_model_depth <int> Bla (default: '30')
-model:model_depth <int> Bla (default: '4')
Parameters of PILISScoring:
-scoring:use_local_scoring ...
-scoring:do_not_use_evalue_scoring ...
-scoring:survival_function_bin_size <int> ... (default: '20')
-scoring:global_linear_fitting_threshold <double> ... (default: '0.1')
-scoring:local_linear_fitting_threshold <double> ... (default: '0.5')
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">+PILISIdentification</span><span class="node_description">performs a peptide/protein identification with the PILIS engine</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 'PILISIdentification'</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 in MzML format</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 file in idXML format</span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">model_file</span><span class="item_value"></span>
<span class="item_description">the model file of the PILISModel</span><span class="item_tags">input file</span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">peptide_db_file</span><span class="item_value"></span>
<span class="item_description">a file which should contain peptides in the format<br>DFPIANGER 1019.09 1<br>where the first column is the peptide, the second the m/z<br>the third the charge. As a alternative the sequence file<br>may contain only peptide sequences each in a separate line<br>repectively</span><span class="item_tags">input file</span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">precursor_mass_tolerance</span><span class="item_value">2</span>
<span class="item_description">the precursor mass tolerance</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">peak_mass_tolerance</span><span class="item_value">1</span>
<span class="item_description">the peak mass tolerance</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">max_pre_candidates</span><span class="item_value">200</span>
<span class="item_description">number of candidates that are used for precise scoring</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">max_candidates</span><span class="item_value">20</span>
<span class="item_description">number of candidates that are reported by PILIS</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">upper_mz</span><span class="item_value">2000</span>
<span class="item_description">upper mz interval endpoint</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">lower_mz</span><span class="item_value">200</span>
<span class="item_description">lower mz interval endpoint</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">fixed_modifications</span><span class="item_value"></span>
<span class="item_description">monoisotopic_mass@residues e.g.: 57.021464@C</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;">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">+++model</span><span class="node_description">Parameters of PILISModel</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">charge_directed_threshold</span><span class="item_value">0.3</span>
<span class="item_description">bla</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">charge_remote_threshold</span><span class="item_value">0.2</span>
<span class="item_description">bla</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">charge_loss_factor</span><span class="item_value">0.5</span>
<span class="item_description">bla</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">min_y_ion_intensity</span><span class="item_value">0.2</span>
<span class="item_description"></span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">min_b_ion_intensity</span><span class="item_value">0.15</span>
<span class="item_description"></span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">min_a_ion_intensity</span><span class="item_value">0.05</span>
<span class="item_description"></span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">min_y_loss_intensity</span><span class="item_value">0.05</span>
<span class="item_description"></span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">min_b_loss_intensity</span><span class="item_value">0.02</span>
<span class="item_description"></span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">visible_model_depth</span><span class="item_value">30</span>
<span class="item_description">bla</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">model_depth</span><span class="item_value">4</span>
<span class="item_description">bla</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">+++scoring</span><span class="node_description">Parameters of PILISScoring</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">use_local_scoring</span><span class="item_value">false</span>
<span class="item_description">...</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;">do_not_use_evalue_scoring</span><span class="item_value">false</span>
<span class="item_description">...</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;">survival_function_bin_size</span><span class="item_value">20</span>
<span class="item_description">...</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">global_linear_fitting_threshold</span><span class="item_value">0.1</span>
<span class="item_description">...</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">local_linear_fitting_threshold</span><span class="item_value">0.5</span>
<span class="item_description">...</span><span class="item_tags"></span><span class="item_restrictions"> </span></div></div>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000034">Todo:</a></b></dt><dd>Check for missing precursors (Hiwi) </dd></dl>
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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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