Types (extension point)

Identifier

ru.biosoft.galaxy.types

Plugin

ru.biosoft.galaxy

Since

0.9.3

Registry

FormatRegistry

Description

This extension point allows to map Galaxy data types to BioUML data types. For each Galaxy file format you should specify BioUML class and (if necessary) importer/exporter combination. If some Galaxy file format is undefined, Generic file importer and exporter are used by default.

Configuration Markup

<!ELEMENT format (exporter?,importer?)>
<!ATTLIST format
   galaxyFormat    CDATA #REQUIRED
   fileExtension   CDATA #REQUIRED
   bioumlType      CDATA #REQUIRED
>

galaxyFormat

name of the Galaxy format as it appears in Galaxy XML tool definition

fileExtension

file extension associated with this format. Usually the same as galaxyFormat.

bioumlType

fully-qualified name of BioUML Java class (must implement DataElement interface).

<!ELEMENT exporter (property*)>
<!ATTLIST exporter
   name    CDATA #REQUIRED
>

name

name of the exporter format (must be registered via ru.biosoft.access.export).

<!ELEMENT importer (property*)>
<!ATTLIST importer
   name    CDATA #REQUIRED
>

name

name of the importer format (must be registered via ru.biosoft.access.import).

<!ELEMENT property>
<!ATTLIST property
   name    CDATA #REQUIRED
   value   CDATA #REQUIRED
>

name

fully qualified name of the bean property of importer/exporter parameter to change

value

value of given property. Registry will attempt to convert it from string to the corresponding type using TextUtil.fromString method.

Example

<format galaxyFormat="tabular" fileExtension="dat" bioumlType="ru.biosoft.table.TableDataCollection">
  <exporter name="Tab-separated text (*.txt)">
    <property name="includeHeaders" value="false"/>
  </exporter>
  <importer name="Tabular (*.txt, *.xls, *.tab, etc.)">
    <property name="headerRow" value="0"/>
    <property name="dataRow" value="1"/>
    <property name="columnForID" value="Generate unique ID"/>
  </importer> 
</format>

This extension defines "tabular" Galaxy format, which maps to BioUML type TableDataCollection ( table). For exporting BioUML element to Galaxy file "Tab-separated text (*.txt)" exporter will be used with "includeHeaders" value set to false. For importing Galaxy result into BioUML "Tabular (*.txt, *.xls, *.tab, etc.)" importer will be used with some options set.