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<div class="title">InclusionExclusionListCreator </div>  </div>
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<div class="textblock"><p>A tool for creating inclusion and/or exclusion lists for LC-MS/MS.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">potential predecessor tools  </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> InclusionExclusionListCreator <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">potential successor tools   </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_MascotAdapter.html">MascotAdapter</a> (or other ID engines)  </td><td valign="middle" align="center" rowspan="2">-   </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FeatureFinderCentroided.html">FeatureFinderCentroided</a>   </td></tr>
</table>
</center><p>Currently this tool can create tab-delimited inclusion or exclusion lists (m/z, RT start, RT stop). The input can either be peptide identifications from previous runs, a feature map or a FASTA-file with proteins. Inclusion and exclusion charges can be specified for FASTA and idXML input. If no charges are specified in the case of peptide id input, only the charge state of the peptide id is in/excluded, otherwise all given charge states are entered to the list.</p>
<p>The RT window size can be specified in the RT section of the INI file, either as relative window with [rt-rel_rt_window_size*rt,rt+rel_rt_window_size*rt] or absolute window.</p>
<p>The default is RT in minutes, but seconds can also be used (see INI file).</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
InclusionExclusionListCreator -- Creates inclusion and/or exclusion lists.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  InclusionExclusionListCreator &lt;options&gt;

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 '*'):
  -include &lt;file&gt;              Inclusion list input file in FASTA or featureXML format. (valid formats: 'feat
                               ureXML', 'fasta')
  -exclude &lt;file&gt;              Exclusion list input file in featureXML, idXML or FASTA format. (valid formats
                               : 'featureXML', 'idXML', 'fasta')
  -out &lt;file&gt;*                 Output file (tab delimited csv file). (valid formats: 'csv')
  -rt_model &lt;file&gt;             RTModel file used for the rt prediction of peptides in FASTA files. (valid 
                               formats: 'txt')
  -pt_model &lt;file&gt;             PTModel file used for the pt prediction of peptides in FASTA files (only neede
                               d for inclusion_strategy PreotinBased_LP). (valid formats: 'txt')
  -inclusion_charges &lt;charge&gt;  List containing the charge states to be considered for the inclusion list comp
                               ounds, space separated. (min: '1')
  -inclusion_strategy &lt;name&gt;   Strategy to be used for selection (default: 'ALL' valid: 'FeatureBased_LP', 
                               'ProteinBased_LP', 'ALL')
  -exclusion_charges &lt;charge&gt;  List containing the charge states to be considered for the exclusion list comp
                               ounds (for idXML and FASTA input), space separated. (min: '1')
  -raw_data &lt;mzMLFile&gt;         File containing the raw data (only needed for FeatureBased_LP). (valid formats
                               : 'mzML')
                               
Common TOPP options:
  -ini &lt;file&gt;                  Use the given TOPP INI file
  -threads &lt;n&gt;                 Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini &lt;file&gt;            Writes the default configuration file
  --help                       Shows options
  --helphelp                   Shows all options (including advanced)

The following configuration subsections are valid:
 - algorithm   Inclusion/Exclusion algorithm section

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">+InclusionExclusionListCreator</span><span class="node_description">Creates inclusion and/or exclusion lists.</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 'InclusionExclusionListCreator'</span></div>
      <div class="item"><span class="item_name" style="padding-left:24px;">include</span><span class="item_value"></span>
<span class="item_description">Inclusion list input file in FASTA or featureXML format.</span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML,*.fasta</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">exclude</span><span class="item_value"></span>
<span class="item_description">Exclusion list input file in featureXML, idXML or FASTA format.</span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML,*.idXML,*.fasta</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 (tab delimited csv 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;">rt_model</span><span class="item_value"></span>
<span class="item_description">RTModel file used for the rt prediction of peptides in FASTA files.</span><span class="item_tags">input file</span><span class="item_restrictions">*.txt</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">pt_model</span><span class="item_value"></span>
<span class="item_description">PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP).</span><span class="item_tags">input file</span><span class="item_restrictions">*.txt</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">inclusion_charges</span><span class="item_value">[]</span>
<span class="item_description">List containing the charge states to be considered for the inclusion list compounds, space separated.</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">inclusion_strategy</span><span class="item_value">ALL</span>
<span class="item_description">strategy to be used for selection</span><span class="item_tags"></span><span class="item_restrictions">FeatureBased_LP,ProteinBased_LP,ALL</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">exclusion_charges</span><span class="item_value">[]</span>
<span class="item_description">List containing the charge states to be considered for the exclusion list compounds (for idXML and FASTA input), space separated.</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">raw_data</span><span class="item_value"></span>
<span class="item_description">File containing the raw data (only needed for FeatureBased_LP).</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML</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">Inclusion/Exclusion algorithm section</span></div>
        <div class="node"><span class="node_name">++++InclusionExclusionList</span><span class="node_description"></span></div>
          <div class="item"><span class="item_name" style="padding-left:40px;">missed_cleavages</span><span class="item_value">0</span>
<span class="item_description">Number of missed cleavages used for protein digestion.<br></span><span class="item_tags"></span><span class="item_restrictions"> </span></div>          <div class="node"><span class="node_name">+++++RT</span><span class="node_description"></span></div>
            <div class="item"><span class="item_name" style="padding-left:48px;">unit</span><span class="item_value">minutes</span>
<span class="item_description">Create lists with units as seconds instead of minutes</span><span class="item_tags"></span><span class="item_restrictions">minutes,seconds</span></div>            <div class="item"><span class="item_name" style="padding-left:48px;">use_relative</span><span class="item_value">true</span>
<span class="item_description">Use relative RT window, which depends on RT of precursor.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>            <div class="item"><span class="item_name" style="padding-left:48px;">window_relative</span><span class="item_value">0.05</span>
<span class="item_description">[for RT:use_relative == true] The relative factor X for the RT exclusion window, e.g. the window is calculated as [rt - rt*X, rt + rt*X].</span><span class="item_tags"></span><span class="item_restrictions">0:10</span></div>            <div class="item"><span class="item_name" style="padding-left:48px;">window_absolute</span><span class="item_value">90</span>
<span class="item_description">[for RT:use_relative == false] The absolute value X for the RT exclusion window in [sec], e.g. the window is calculated as [rt - X, rt + X].</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>          <div class="node"><span class="node_name">+++++merge</span><span class="node_description"></span></div>
            <div class="item"><span class="item_name" style="padding-left:48px;">mz_tol</span><span class="item_value">10</span>
<span class="item_description">Two inclusion/exclusion windows are merged when they (almost) overlap in RT (see 'rt_tol') and are close in m/z by this tolerance. Unit of this is defined in 'mz_tol_unit'.</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>            <div class="item"><span class="item_name" style="padding-left:48px;">mz_tol_unit</span><span class="item_value">ppm</span>
<span class="item_description">Unit of 'mz_tol'</span><span class="item_tags"></span><span class="item_restrictions">ppm,Da</span></div>            <div class="item"><span class="item_name" style="padding-left:48px;">rt_tol</span><span class="item_value">1.1</span>
<span class="item_description">Maximal RT delta (in seconds) which would allow two windows in RT to overlap (which causes merging the windows). Two inclusion/exclusion windows are merged when they (almost) overlap in RT and are close in m/z by this tolerance (see 'mz_tol'). Unit of this param is [seconds].</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>        <div class="node"><span class="node_name">++++PrecursorSelection</span><span class="node_description"></span></div>
          <div class="item"><span class="item_name" style="padding-left:40px;">ms2_spectra_per_rt_bin</span><span class="item_value">5</span>
<span class="item_description">Number of allowed MS/MS spectra in a retention time bin.</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</span></div>          <div class="item"><span class="item_name" style="padding-left:40px;">min_peak_distance</span><span class="item_value">3</span>
<span class="item_description">The minimal distance (in Da) of two peaks in one spectrum so that they can be selected.</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>          <div class="item"><span class="item_name" style="padding-left:40px;">selection_window</span><span class="item_value">2</span>
<span class="item_description">All peaks within a mass window (in Da) of a selected peak are also selected for fragmentation.</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>          <div class="item"><span class="item_name" style="padding-left:40px;">exclude_overlapping_peaks</span><span class="item_value">false</span>
<span class="item_description">If true overlapping or nearby peaks (within min_peak_distance) are excluded for selection.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>          <div class="node"><span class="node_name">+++++Exclusion</span><span class="node_description"></span></div>
            <div class="item"><span class="item_name" style="padding-left:48px;">use_dynamic_exclusion</span><span class="item_value">false</span>
<span class="item_description">If true dynamic exclusion is applied.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>            <div class="item"><span class="item_name" style="padding-left:48px;">exclusion_time</span><span class="item_value">100</span>
<span class="item_description">The time (in seconds) a feature is excluded.</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>          <div class="node"><span class="node_name">+++++ProteinBasedInclusion</span><span class="node_description"></span></div>
            <div class="item"><span class="item_name" style="padding-left:48px;">max_list_size</span><span class="item_value">1000</span>
<span class="item_description">The maximal number of precursors in the inclusion list.</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</span></div>            <div class="node"><span class="node_name">++++++rt</span><span class="node_description"></span></div>
              <div class="item"><span class="item_name" style="padding-left:56px;">min_rt</span><span class="item_value">960</span>
<span class="item_description">Minimal rt in seconds.</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>              <div class="item"><span class="item_name" style="padding-left:56px;">max_rt</span><span class="item_value">3840</span>
<span class="item_description">Maximal rt in seconds.</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>              <div class="item"><span class="item_name" style="padding-left:56px;">rt_step_size</span><span class="item_value">30</span>
<span class="item_description">rt step size in seconds.</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</span></div>              <div class="item"><span class="item_name" style="padding-left:56px;">rt_window_size</span><span class="item_value">100</span>
<span class="item_description">rt window size in seconds.</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</span></div>            <div class="node"><span class="node_name">++++++thresholds</span><span class="node_description"></span></div>
              <div class="item"><span class="item_name" style="padding-left:56px;">min_protein_id_probability</span><span class="item_value">0.95</span>
<span class="item_description">Minimal protein probability for a protein to be considered identified.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div>              <div class="item"><span class="item_name" style="padding-left:56px;">min_pt_weight</span><span class="item_value">0.5</span>
<span class="item_description">Minimal pt weight of a precursor</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div>              <div class="item"><span class="item_name" style="padding-left:56px;">min_mz</span><span class="item_value">500</span>
<span class="item_description">Minimal mz to be considered in protein based LP formulation.</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>              <div class="item"><span class="item_name" style="padding-left:56px;">max_mz</span><span class="item_value">5000</span>
<span class="item_description">Minimal mz to be considered in protein based LP formulation.</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>              <div class="item"><span class="item_name" style="padding-left:56px;">use_peptide_rule</span><span class="item_value">false</span>
<span class="item_description">Use peptide rule instead of minimal protein id probability</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div>              <div class="item"><span class="item_name" style="padding-left:56px;">min_peptide_ids</span><span class="item_value">2</span>
<span class="item_description">If use_peptide_rule is true, this parameter sets the minimal number of peptide ids for a protein id</span><span class="item_tags"></span><span class="item_restrictions">1:&#8734;</span></div>              <div class="item"><span class="item_name" style="padding-left:56px;">min_peptide_probability</span><span class="item_value">0.95</span>
<span class="item_description">If use_peptide_rule is true, this parameter sets the minimal probability for a peptide to be safely identified</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div></div>
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