<command> tag in xml file for a C++ tool

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<command> tag in xml file for a C++ tool

vs49
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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Re: <command> tag in xml file for a C++ tool

Peter Cock
On Wed, May 22, 2013 at 5:21 PM, vijayalakshmi <[hidden email]> 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
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Re: <command> tag in xml file for a C++ tool

James Taylor
In reply to this post by vs49
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 <[hidden email]> 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.
>
>
> ___________________________________________________________
> 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/
___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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