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Parameters in GUI
Parameter | Description | Default value |
---|---|---|
Genome file | Select a genome file (sqlite3 file) to search refGenes. (--genome). | hg19 |
Output file | Select which type of genes need to output. up for genes upstream to peak summit, down for genes downstream to peak summit, all for both up and down. (--op). | all |
Official gene symbols | Output official gene symbol instead of refseq name. (--symbol). | False |
Distance | Set a number which unit is base. It will get the refGenes in n bases from peak center. (--distance). | 3000 |
Parameters in
Schema FileWorkflow File
Type: peak2gene-id
Parameter | Parameter in the GUI | Type |
---|---|---|
genome | Genome file | string |
outpos | Output file | string |
symbol | Official gene symbols | boolean |
distance | Distance | numeric |
Input/Output Ports
The element has 1 input port:
Name in GUI: Peak2gene data
Name in Schema File Workflow File: in-data
Slots:
Slot In GUI | Slot in Schema Workflow File | Type |
---|---|---|
Treatment features | _treat-ann | ann-table-list |
And 1 output port:
Name in GUI: Peak2gene output data
Name in Schema File Workflow File: out-data
Slots:
Slot In GUI | Slot in Schema Workflow File | Type |
---|---|---|
Gene regions | gene-annotation | ann-table-list |
Peak regions | peak-annotation | ann-table-list |