Broad: Annotation: Argo: Help: XML Start File Format

What is an Argo xml start file?

Argo start xml files can be used to open argo on specified sequence and track data files. This is particularly useful when running argo via java webstart.

The top node is called "argo." This node may contain sequence_perspective and comparative_perspective nodes. Each of these nodes opens a perspective window based on the data files specified in their subnodes.

Specify the argo start file by setting the system property "calhoun.argo.startfile" to the desired url.


java -jar -D argo.jar


java -jar -Dlocal/argo/start.xml argo.jar

Sequence Perspective

Take a look at this example start file.

The sequence_perspective node may contain one or more sequence nodes. Each sequence node will be opened in a separate tab. The sequence node must have a name, a sequence file url, and a data type for the sequence file (like "fasta"). An optional "offset" parameter may also be specified. Argo will treat the first sequence residue as being at position in file + offset.

Each sequence node may contain one or more track nodes. Track nodes require a name, a track file url, data type (like "gff3") and a hex color. An optional url template parameter provides lets you specify a web link to open when a feature on this track is double clicked. Alphanumeric values preceded by a dollar sign are treated as case insensitive placeholders for the interpolation of corresponding feature attribute values.

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