...
Parameters in GUI
| Parameter | Description | Default value |
|---|---|---|
| Output directory | Directory to save MACS output files. | |
| Reference annotation | Merge the input assemblies together with this reference annotation. | |
| Reference sequence | The genomic DNA sequences for the reference. It is used to assist in classifying transfrags and excluding artifacts (e.g. repeats). For example, transcripts consisting mostly of lower-case bases are classified as repeats. | |
| Minimum isoform fraction | Discard isoforms with abundance below this. | 0.05 |
| Cuffcompare tool path | The path to the Cuffcompare external tool in UGENE. | default |
| Cuffmerge tool path | The path to the Cuffmerge external tool in UGENE. | default |
| Temporary directory | The directory for temporary files. | default |
Parameters in
Schema FileWorkflow File
Type: cuffmerge
| Parameter | Parameter in the GUI | Type |
|---|---|---|
| out-dir | Output directory | string |
| ref-annotation | Reference annotation | string |
| ref-seq | Reference sequence | string |
| min-isoform-fraction | Minimum isoform fraction | numeric |
| cuffcompare-tool-path | Cuffcompare tool path | string |
| path | Cuffmerge tool path | string |
| tmp-dir | Temporary directory | string |
Input/Output Ports
The element has 1 input port:
Name in GUI: Set of annotations
Name in Schema File Workflow File: in-assembly
Slots:
| Slot In GUI | Slot in Schema Workflow File | Type |
|---|---|---|
| Set of annotations | in-annotations | ann_table |
And 1 output port:
Name in GUI: Set of annotations
Name in Schema File Workflow File: out-assembly
Slots:
| Slot In GUI | Slot in Schema Workflow File | Type |
|---|---|---|
| Set of annotations | out-annotations | ann_table |