Pladipus-Search
Pladipus-search is a sequence database searching module.
Note that the discussed parameters are the ones mandatory for pladipus execution. For more detailed parameters, please refer to the respective pages.
1. SearchSetupStep
This step preprocesses the input data in order to prepare the worker for executing a sequence database search using SearchGUI’s command line. This step will download and unzip the required resources to the temp/search/resources folder in the pladipus home folder.
The following parameters are required:
| Parameter | Meaning |
|---|---|
| spectrum_files | input spectrum file (mgf or mgf.zip) or the folder containing mgf files |
| id_params | parameter file generated by SearchGUI |
| fasta_file | sequence database file in FASTA format |
2. SearchGUIStep
This step manages the execution of SearchGUI’s command line. It requires the following parameters (next to the ones specified by the SearchGUI command line). This step will also automatically download the latest SearchGUI version specific for the machine’s OS in case it is absent on the system..
| Parameter | Meaning |
|---|---|
| spectrum_files | input spectrum file (mgf or mgf.zip) or the folder containing mgf files |
| id_params | parameter file generated by SearchGUI |
| fasta_file | sequence database file in FASTA format |
3. PeptideShakerStep
This step manages the execution of PeptideShaker command line. This step will also automatically download the latest PeptideShaker version in case it is absent on the system.
| Parameter | Meaning |
|---|---|
| output_folder | the output folder for the result files |