Command Line Arguments
| Name | Argument | Short Description | Group |
|---|---|---|---|
| Gene Ontology Structure | -useobo | Provide a specific version of the Gene Ontology Structure. | Other |
| Enzyme Data | -enzclass and -enzymedat | Provide a specific version of the enzyme databases. | Other |
| Create Properties File | -createproperties | Creates a properties file necessary to run Blast2GO CLI. | Other |
| Create Key File | -createkeyfile | Create the key file necessary activation of the product. | Other |
| Cloud Unit Balance | -cloudunitbalance | Consult the balance of CloudUnits. | Other |
| Workspace Location | -workspace | Provide a workspace folder. | Other |
| Generic Data Export | -exportgeneric | Customize which data you want to export. | Save/Export |
| Create PDF Report | -savereport | Create a PDF report. | Save/Export |
| Export Annotations | -saveannot | Export GO and EC annotations. | Save/Export |
| Save Project | -savebox | Save the project in .box format. | Save/Export |
| Save Sequence Table | -saveseqtable | Export the projects sequence table. | Save/Export |
| Save Longest Open Reading Frame | -savelorf | Save the longest ORFs to a Fasta file. | Save/Export |
| Charts and Statistics | -statistics | Create charts for the data provided. | Analysis |
| GO-Slim | -goslim | Generalize GO annotations with GO-Slim. | Analysis |
| EC-Code Mapping | -ecmapping | Map GOs to EC-Codes. | Analysis |
| GO Annotation | -annotation | Run GO Annotation. | Analysis |
| GO Mapping | -mapping | Run GO Mapping. | Analysis |
| EBI InterProScan | -ips | Run EBI InterProScan | Analysis |
| Local Blast | -localblast | Run Blast on the local machine. | Analysis |
| CloudInterProScan | -cloudips | Run CloudInterProScan. | Analysis |
| CloudBlast | -cloudblast | Run CloudBlast. | Analysis |
| Load Project | -loadbox or -loadb2g | Load an OmicsBox/Blast2GO Project file. | Load/Import |
| Load InterProScan Results | -loadips48 or -loadips50 | Load InterProScan results in .XML format. | Load/Import |
| Load Annotations | -loadannot | Load annotation results in .annot format. | Load/Import |
| Load Blast Results | -loadblast or -loadblast31 | Load Blast Results in various formats. | Load/Import |