On Wed, May 22, 2013 at 5:21 PM, vijayalakshmi <v...@buffalo.edu> wrote:
> 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.

For a compiled binary there is no interpreter, just use <command>. e.g.

<command>IntersectBed -a $inputreads -b $inputgenes ...</command>

I presume there are more options to your command, e.g. output files ;)

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