How To Integrate Tools: Bismark, Fastqc, Fastq Tools, Fastx, Trim Galore?

Question

[Sam ad]

Hello! I would like to integrate these great tools : Bismark, FastQC, FastQ Tools, FastX, Trim Galore in Galaxy. I know it's possible and not that hard. Can someone guide to how to do integrate these tools into Galaxy? Thanks in advance.

Answer 1

[Istvan Albert]

You should consult the tutorial here:

http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial

Basically the most important step is that of writing the so called tool definition file (step 3) in the tutorial. This an XML file that describes both what the interface looks like inside Galaxy and what invocation of the tool is.

[Michael]

Just saw that there is no xml schema definition for the tool format, maybe somebody made one? If not, it might be best to start with an existing file as a template and edit it in an xml-editor, e.g. eclipse. There are already several FastQ tools in the public instance, so maybe based on one of these.

[Istvan Albert]

I think the schema would be very complex write (or understand) as over the years the format has evolved from just simple descriptive fields to support complex multi-step (wizard type) interfaces and other dynamic fields. As you suggest it is best to start with and modify the simple tool files that are already there.

Here is the list of accepted fields:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax

[Sam ad]

Thanks for the answer. I am stuck in the interface part. How do I know which fields to include? i need to understand the tool deeply from inside for this, rite?

[Michael]

I guess reading the documentation will be quite sufficient most of the time ;)

Answer 2

[Björn]

Just as reference. Trim Galore and Bismark is wrapped and in the official toolshed.