Creating Galaxy tool

If you have BioUML server installed and Galaxy installed, you can add your own tools to BioUML.

Customizing tools menu

If you properly integrated Galaxy with BioUML, Galaxy tools appear in BioUML repository under analyses/Galaxy path. This subtree is populated from Galaxy tool_conf.xml file.

Let's assume that $GALAXY_DIST points to the root folder of Galaxy installation. Look into $GALAXY_DIST/tool_conf.xml file. It contains a number of sections which may contain a number of sections which look like this:

<section name="Section title" id="section_id">
   <tool file="tool/my_tool.xml" />
   <label text="My label" id="my_label"/>
   <tool file="tool/my_other_tool.xml" />
</section>

In BioUML interface section is transformed into folder and label is rendered as a separator between tools. You can freely add, delete or rearrange sections, labels or tools here. To add new tool you should specify a path to the tool description XML file relative to $GALAXY_DIST/tools directory.

Creating your own tool

When you added a link to new tool description XML file, you should create that file. Refer to Galaxy Wiki to learn how to create such files. Please note that not all Galaxy features are supported by BioUML. Ask for technical support if you have any doubts.

Reloading tool configuration

Once you finish editing a tool you should reload Galaxy configuration. You can do this using Script viewpart in BioUML interface and typing the following command here:

galaxy.reload();

Please note that for security reasons this command is available for BioUML server administrators only.