Up: Component summary
Up: Component summary
Function
EnsemblChromosomesRetrieves the Ensembl names and lengths of chromosomes. The organism is given in the connection input where the query database is defined. Currently human and mouse databases are supported.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Annotation |
| Authors | Riku Louhimo (Riku.Louhimo@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Source files | component.xml function.scala |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| connection | Properties | Mandatory | Ensembl database connection configuration file. |
Outputs| Name | Type | Description |
|---|---|---|
| chromosomes | CSV | Ensembl default chromosome names and sizes. |
| extraChr | CSV | All non-default (non-canonical) chromosomes from Ensembl. |
Test cases| Test case | Parameters▼ | IN connection |
OUT chromosomes |
OUT extraChr |
|---|---|---|---|---|
| case1 | (missing) | connection | chromosomes | extraChr |
| case2_mus | (missing) | connection | chromosomes | (missing) |