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Type:
New Feature
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Status: Closed
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Priority:
Major
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Resolution: Won't Fix
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Affects Version/s: None
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Fix Version/s: None
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Component/s: None
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Labels:
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Story Points:5
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Sprint:DEV-37-3
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Affect Type:Userdefined
Element name and description
- Name of the element: "Extract Consensus from Sanger Alignment"
- Description of the element on the Scene: "Extract the consensus sequence from the incoming Sanger alignment(s) to the format_name format."
- Description of the element in the Property Editor: "Extract the consensus sequence from the incoming Sanger alignment."
Input data
There is one input port:
| Item | Value |
|---|---|
| Port name in GUI | Input Sanger alingment |
| Port description | A Sanger alignment which consensus should be extracted |
| Port ID in UWL | mca-in |
| Number of slots | 1 |
| Slot #1 name in GUI | Multiple Chromatogram Alignment URL |
| Slot #1 ID in UWL | mca-url |
| Slot #1 data type | String |
Output data
There are two output ports, but only one is visible:
| Item | Value |
|---|---|
| Port name in GUI | Consensus sequence |
| Port description | Provides resulting consensus as a sequence |
| Port ID in UWL | mca-out-seq |
| Number of slots | 1 |
| Slot #1 name in GUI | Sequence |
| Slot #1 ID in UWL | mca-cons-seq |
| Slot #1 data type | Sequence |
| Item | Value |
| Port name in GUI | Consensus plain text |
| Port description | Provides resulting consensus as a text file |
| Port ID in UWL | mca-out-pt |
| Number of slots | 1 |
| Slot #1 name in GUI | Plain text |
| Slot #1 ID in UWL | mca-cons-pt |
| Slot #1 data type | String |
Parameters
| # | Parameter | Description | Value in GUI | Default value | Note |
|---|---|---|---|---|---|
| 1 | File format | The format of the output file. | A combo box with 2 values: "Plain text" and "FASTA". | Plain text | Depends on this parameter, one or another output port is visible |
| 2 | Keep gaps | Set this parameter if the result consensus must keep the gaps. | A combo box with 2 values: "True" and "False". | True | |
| 3. | Export region | Export the all consensus area or consensus areas of selected reads | A combo box with 2 values: "Export all consensus" and "Export read(s) consensus" | Export all consensus | Depends on this value, the "Reads" parameter either visible or not |
| 4 | Read(s) | Read(s), which consensus areas should be exported | A combo box with check boxes of all input read names (we don't know which of them will be mapped correctly) | All reads are checked |