IDEvaluator

Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.

An arbitrary number of idXML files resulting from a target+decoy search can be provided as input.

Since the q-value can be computed independently from a scoring scheme, no further preprocessing (like IDPep or FDR) is required, apart from a target-decoy annotation! I.e., apply PeptideIndexer to the immediate output of a search engine (or ConsensusID) and use this as input to this tool.

Note

Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

libpng warning: iCCP: known incorrect sRGB profile

IDEvaluator -- Computes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifi
cations for a certain q-value.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

Usage:
  IDEvaluator <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript
ion or use the --helphelp option.

Options (mandatory options marked with '*'):
  -in <file>             Input file(s) (valid formats: 'idXML')
  -out <file>            Output file (if given, no GUI will be displayed) (valid formats: 'png', 'jpg', 'svg'
                         )
  -out_type <file type>  The image format. Set this if you want to force a format not reflected by the 'out' 
                         filename. (valid: 'png', 'jpg', 'svg')
  -out_csv <file>        Optional output of points as table for manual post-processing. (valid formats: 'csv'
                         )
  -q_min <float>         Minimal q-value in plot. (default: '0' min: '0' max: '1')
  -q_max <float>         Maximal q-value in plot. (default: '0.4' min: '0' max: '1')
                         
Common UTIL 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   Additional parameters for FDR and image sizes.

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.

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+IDEvaluatorComputes a 'q-value vs. #PSM' plot which is saved as an image to visualize the number identifications for a certain q-value.

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'IDEvaluator'

in[] Input file(s)input file*.idXML

out Output file (if given, no GUI will be displayed)output file*.png,*.jpg,*.svg

out_type The image format. Set this if you want to force a format not reflected by the 'out' filename.png,jpg,svg

out_csv Optional output of points as table for manual post-processing.output file*.csv

q_min0 Minimal q-value in plot.0:1

q_max0.4 Maximal q-value in plot.0:1

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

forcefalse Overwrite tool specific checks.true,false

testfalse Enables the test mode (needed for internal use only)true,false

+++algorithmAdditional parameters for FDR and image sizes.

++++fdr

use_all_hitsfalse If 'true' not only the first hit, but all are used (peptides only)true,false

++++image

height800 Height of raster images (e.g., PNG).

width1024 Width of raster images (e.g., PNG).