Adds one or several marks to the input sequence depending on the sequence properties. Use this element, for example, in conjunction with the Filter element.
Parameters in GUI
To create a new marker group that would mark the input sequence, select the Add button in the Parameters area. The Create Marker Group dialog appears:
Choose a type of the marker group and input a marker group name. The following types are available:
Length markers — marks a sequence by length. The sequence is marked, for example, if its length is less or greater than the specified value.
Sequence name markers — marks a sequence by a sequence name.
Annotations count markers — marks a sequence by the number of annotations.
Qualifier integer value markers — marks a sequence by the number of integer qualifiers.
Qualifier text value markers — marks a sequence by the number of text qualifiers.
Qualifier float value markers — marks a sequence by the number of float qualifiers.
Text markers — marks a sequence by a file name. For example, if the name:
- starts with the specified text;
- ends with the specified text;
- contains the specified text;
- matches the specified regular expression .
Each marker group can contain more than one marker. Use the Add, Edit and Remove buttons in the dialog to create, modify and delete markers in the marker group.
To edit the created marker group, select the group in the Parameters area and click Edit:
To remove a marker group select it in the list and click Remove.
Parameters in Workflow File
Type: mark-sequenceInput/Output Ports
The element has 1 input port:
Name in GUI: Sequence
Name in Workflow File: in-sequence
Slots:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Sequence | sequence | sequence |
| Location | url | string |
| Set of annotations | annotations | annotation-table-list |
The element has 1 output port.
Name in GUI: Marked sequence
Name in Workflow File: out-marked-seq
Slots:
Each created marker group adds a text slot with the following properties:
| Slot In GUI | Slot in Workflow File | Type |
|---|---|---|
| Name of the marker group | Name of the marker group | string |