Pladipus-Denovo
Pladipus-denovo is a denovo sequence identification module.
Note that the discussed parameters are the ones mandatory for pladipus execution. For more detailed parameters, please refer to the respective pages.
1. DeNovoGUISetupStep
This step preprocesses the input data in order to prepare the worker for executing a de novo database search procedure using DeNovoGUI’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 |
2. DenovoGUIStep
This step manages the execution of DenovoGUI’s command line. It requires the following parameters (next to the ones specified by the DenovoGUI command line). This step will also automatically download the latest DenovoGUIStep version.
| Parameter | Meaning |
|---|---|
| spectrum_files | input spectrum file (mgf or mgf.zip) or the folder containing mgf files |
| id_params | parameter file generated by DenovoGUI |
| output_folder | the output folder for results |