<command> tag in xml file for a C++ tool
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.
On Wed, May 22, 2013 at 5:21 PM, vijayalakshmi <vs49@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
You might find it instructive to look at the existing bedtools wrappers here: http://toolshed.g2.bx.psu.edu/view/aaronquinlan/bedtools -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, May 22, 2013 at 12:21 PM, vijayalakshmi <vs49@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.
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participants (3)
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James Taylor -
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vijayalakshmi