Adding Reference Genome, Reference Sequence, and Reference Annotation fields

You can add fields for reference genomes, only reference sequences, and only reference annotations to your app.

Reference Genome fields

1. Unable to render {include} The included page could not be found.
2. Click to open the section into which you want to add the genome field.
3. In the Reference Genome section on the left, click and drag the Reference Genome item to the location in the selected section.
4. Click in the Reference Genome Label field to display its Details on the right.
5. Edit the Details section:
   • Reference Genome Selector label: Edit the label as you want it to be displayed in the DE.
   • Argument option: Enter the command line option according to the tool's requirements.
   • Default item to display: Select the default genome.
   • Make this field required: Requires the user to select a reference genome.
   • Exclude this item if nothing is entered: Skips the item when no selection has been made.
   • Tool tip text: Edit as needed.
6. Click Preview and then click Preview UI. When done, close the Preview window.
7. Click Save.

Reference Sequence fields

1. In the Create Apps window for the app, click to open the section into which you want to add the sequence field.
2. In the Reference Genome section on the left, click and drag the Reference Sequence item to the location in the selected section.
3. Click in the Reference Sequence Label field to display its Details on the right.
4. In the Details section:
   • Reference Sequence Selector label: Edit the label as you want it to be displayed in the DE.
   • Argument option: Enter the command line option according to the tool's requirements.
   • Default item to display: Select the default reference sequence.
   • Make this field required: Requires the user to select a reference sequence.
   • Exclude this item if nothing is entered: Skips the item when no selection has been made.
   • Tool tip text: Edit as needed.
5. Click Preview and then click Preview UI. When done, close the Preview window.
6. Click Save.

Reference Annotation fields

1. In the Create Apps window for the app, click to open the group into which you want to add the annotation field.
2. In the Reference Genome section on the left, click and drag the Reference Annotation item to the location in the selected section.
3. Click in the Reference Annotation Label field to display its Details on the right.
4. In the Details section:
   • Reference Annotation Selector label: Edit the label as you want it to be displayed in the DE.
   • Argument option: Enter the command line option according to the tool's requirements.
   • Default item to display: Select the default reference sequence.
   • Make this field required: Requires the user to select a reference annotation.
   • Exclude this item if nothing is entered: Skips the item when no selection has been made.
   • Tool tip text: Edit as needed.
5. Click Preview and then click Preview UI. When done, close the Preview window.
6. Click Save.

Deleting a reference genome, sequence, or annotation field

1. In the middle section, hover over the argument to delete until you see a blue border around it:
   
2. Hover over the the gray icon at the top right until it turns red:
   
3. Click the icon to complete the deletion.
4. Click Save.