Hi VJ, bedtools is not new. It is in already available through the toolshed. Here are a few relevant links: http://wiki.galaxyproject.org/Tool%20Shed http://testtoolshed.g2.bx.psu.edu/view/bgruening/bedtools_test_bag Furthermore, the bedtool maintainer offers wrappers from his main website. The above bedtools are a patched version of his wrappers, waiting for approval. Cheers, Bjoern

Hi all,

I want to include a new tool to galaxy. The tool is written in C ++. How do I write the xml file to execute a cpp program? The tool that I am trying to integrate is https://code.google.com/p/bedtools/

I have the class file to be executed and the command to execute it. For example,

'IntersectBed' is my class file. The command to execute it is $intersectBed -a reads.bed -b genes.bed (reads.bed and genes.bed are input files provided by the user)

How should I write the <command> tag in the xml file so as to execute the above command? Since C++ is complied as opposed to Python which is interpreted, I am not sure how to write the <command> tag.

I am a newbie. I appreciate any guidance offered!

Thanks, VJ. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/