12/26/2023 0 Comments Searchgui referenceThese cover many aspects, from general utility functions and macros to input/output functions and dynamic memory management functions: Here is an example for Windows using a search parameters file.The elements of the C language library are also included as a subset of the C++ Standard library. Please refer to this file when forwarding the SearchGUI search results to PeptideShaker. The list of MGF files used in the search (after splitting) is always listed in the file output_folder\searchGUI_input.txt. However, if a tool such as PeptideShaker is used to combine the search results afterwards, the effects of the splitting should be minimal. This option should only be used if you are experiencing memory issues with the search engines, as it is always best to search the complete MGF files in a single search. SearchGUI therefore provides an option to split the MGF files. If the provided MGF files become too big it can result in memory issues for the search engines, e.g., OMSSA often struggles with files bigger than 1GB. ref_mass Reference mass for the conversion of the fragment ion tolerance from ppm to Dalton. Default is the number of cores available. threads The number of threads to use for the processing. 19.0 ) ( 0 : no correction, 1 : add missing spectrum titles, default is '0' ). missing_titles Add missing spectrum titles. ( 0 : no correction, 1 : rename spectra, 2 : delete spectra, default is '1' ). correct_titles Correct for duplicate spectrum titles. ) - mgf_spectrum_count The maximum number of spectra per mgf file when splitting. mgf_splitting The maximum mgf file size in MB before splitting an mgf. mgf_check_size Turn the mgf size check on or off. makeblastdb_folder The folder where makeblastdb is installed, defaults to the provided version for the given OS. directag_folder The folder where DirecTag is installed, defaults to the provided version for the given OS. novor_folder The folder where Novor is installed, defaults to the provided version for the given OS. metamorpheus_folder The folder where MetaMorpheus is installed, defaults to the provided version for the given OS. andromeda_folder The folder where Andromeda is installed, defaults to the provided version for the given OS. tide_folder The folder where Tide is installed, defaults to the provided version for the given OS. comet_folder The folder where Comet is installed, defaults to the provided version for the given OS. omssa_folder The folder where OMSSA is installed, defaults to the provided version for the given OS. msgf_folder The folder where MS - GF + is installed. ms_amanda_folder The folder where MS Amanda is installed, defaults to the provided version for the given OS. myrimatch_folder The folder where MyriMatch is installed, defaults to the provided version for the given OS. xtandem_folder The folder where X ! Tandem is installed, defaults to the provided version for the given OS. In distributed setups, we recommend keeping a clean copy of SearchGUI, and distribute it to the different workers prior to execution. It is thus important to use a single instance of SearchCLI at a time. Please note that the search engines use indexes and temporary files stored locally in their folders. We recommend redirecting temporary folders and logs when running SearchGUI on the command line. Alternatively, the parameters can be passed directly to SearchCLI by using the command line arguments of the IdentificationParametersCLI. Identification parameter files are in the json format and can be created in the graphical user interface, using the IdentificationParametersCLI, or using third party tools. Identification parameters for use in SearchCLI can be provided as a file. SearchCLI searches spectrum files according to search parameters using X! Tandem, MyriMatch, MS Amanda, MS-GF+, OMSSA, Comet, Tide, Andromeda, MetaMorpheus, Novor and DirecTag. The command line interface to SearchGUI, referred to as SearchCLI, makes it possible to run all search engines and de novo algorithms supported by SearchGUI using a single command line. SearchCLI SearchGUI Command Line Interface
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