Since version 1.5, the Taverna workflow system has a
plugin
mechanism
which enables the software to be tailored
to specific scientific domains. The following Taverna
plugins have been developed here at the
MCISB for use in systems biology and informatics in
general:
PDFRenderer -
enables Taverna to display PDF files
CSVRenderer - allows
Taverna to display files in comma separated values
format as a table
Excel2CSVReader
- a local java processor which outputs a comma
separated values String from a worksheet in an Excel
file
PDFRenderer
This plugin is a renderer which can be used for viewing
PDF documents from the Taverna workbench. The following
steps are required to install this plugin:
Click on Tools > Plugin Manager
Click on the 'Find New Plugins' button and add a New
Plugin Site by entering "MCISB" as site name
and
"http://dbk-ed.mib.man.ac.uk/taverna/1.7/plugins/"
as the site URL then click OK
Click on PDF Renderer followed by install. This
plugin will now be downloaded and installed
To enable the display of PDF documents in Taverna, the data
must be tagged with a MIME type of 'application/pdf'.
Screenshot showing how the results of the R
data analysis workflow using the PDFViewer plugin to
display final output.
CSVRenderer
This plugin is a renderer which can be used for viewing CSV
documents which have been generated from Taverna
workflows. To install
this plugin:
Click on Tools > Plugin Manager
Click on the 'Find New Plugins' button and add a New Plugin
Site by entering "MCISB" as site name
and "http://dbk-ed.mib.man.ac.uk/taverna/1.7/plugins/" as
the site URL then click OK
Click on CSVRenderer followed by install. This plugin will
now be downloaded and installed
To enable
the display of CSV documents in Taverna, the data must be
tagged with a MIME type of 'text/csv'.
The tabular display
can then be selected by pressing shift and left clicking the
results CSV object and selecting view as comma separated
values.
Screenshot showing how this renderer displays CSV documents.
Excel2CSVReader
This plugin is a local Java processor which can be used
for reading specfic worksheets from Excel files into a
CSV document as part of a workflow. The following
steps are required to install this plugin:
Click on Tools > Plugin Manager
Click on the 'Find New Plugins' button and add a New
Plugin Site by entering "MCISB" as site name
and
"http://dbk-ed.mib.man.ac.uk/taverna/1.7/plugins/"
as the site URL then click OK
Click on Excel2CSVReader followed by install. This
plugin will now be downloaded and installed
Once Taverna has been re-started, this processor
will be available in the service palette under the
local services > local java widgets > io directory.
This processor requires 2 inputs, the path to an Excel
file on your local file system and the worksheet number in the
Excel file
that you want outputted as a CSV document:
An example workflow using the Excel2CSVReader processor.
