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.

version1.10.0 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

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).