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 ;) Peter ___________________________________________________________ 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/