what is the procedure/requirements for registering a tool with Galaxy? Is there a technical manual on how this can be done? Links would be appreciated.
For starters you will need to write an XML wrapper. This XML wrapper will tell Galaxy how to build the form that the user sees for specifying parameters. On the server side, it will tell Galaxy which program to run and what parameters to use.
For some tools, like the Picard suite, there are supplementary wrappers called through the XML wrapper which are used to handle the logic for building more complicated command line calls. You can write these in any language you want as long as the host can run the script or executable. Basically, Galaxy calls the supplementary wrapper and passes parameters to it. That supplementary wrapper then takes those parameters and uses them to build and run a sophisticated command line, and then runs that line so that Galaxy can know when the process has completed.
What I would recommend is looking at the pre-existing wrappers on a local Galaxy instance, if you have access to it. They're in the tools/ subfolder of the galaxy installation root. What also really helped me was this tutorial video.
HTH!
In addition to Deedee's overview you'll want to check our the add a tool tutorial, as well as the comprehensive list of tool config file syntax. These two pages should give you all the information you need to add a tool to Galaxy. The suggestion of looking at existing tools is great. The Picard tools are well defined and would provide a comprehensive example of what these tool config definitions look like. If you want to make your work available to other Galaxy users you need to set up a local tool shed to test your work, and then push your work to the public tool shed.
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