Hi Lifeng

I am glad to hear it works 

WRT your thoughts about using a wrapper script for each tool: I agree it might 
help you to standardize your tools, however it also introduces an extra step, 
which needs to be taken care of if  you want to change/upgrade your tool. 
Personally, I would only use a wrapper if it is necessary or it adds some 
benefits for the tool.  Others on the list might have a different opinion?

Hans-Rudolf



On Mar 25, 2014, at 3:13 PM, Lifeng Lin wrote:

> works like a charm. Thank you!
> I start to wonder if i should use this wrapper approach on all scripts 
> regardless of the original input-output format for standardized integration, 
> and possible automated integrations in the future.
> 
> 
> On Tue, Mar 25, 2014 at 6:53 AM, Hans-Rudolf Hotz <hansrudolf.h...@fmi.ch> 
> wrote:
> Hi Lifeng
> 
> The easiest way to execute your script will be to provide a wrapper script 
> (written in your preferred language, eg Python, perl, etc). Call the wrapper 
> script like this:
> 
> <command>wrapper $input $output1 $output2</command>
> 
> and define $output1 $output2 according to your needs: format="fasta", 
> format="txt"
> 
> 
> the wrapper will call your script and rename/move the output.
> 
> 
> Hope this helps,
> Regards, Hans-Rudolf
> 
> 
> On Mar 25, 2014, at 3:23 AM, <galaxy-user-boun...@lists.bx.psu.edu> 
> <galaxy-user-boun...@lists.bx.psu.edu> wrote:
> 
> >
> > From: Lifeng Lin <linlif...@gmail.com>
> > Date: March 25, 2014 12:58:52 AM GMT+01:00
> > To: <galaxy-u...@lists.bx.psu.edu>
> > Subject: Question concerning the xml file for local tools with multiple 
> > output files.
> >
> >
> > Hi folks,
> >
> > I am trying to integrate some of my local Perl scripts into a downloaded 
> > instance of Galaxy. So far the script with a simple "in_file to out_file" 
> > format worked great, but I am having problems understanding how to treat 
> > scripts with multiple output files that share the same input argv.
> > for example: the script run like this in command line:
> >
> > <script name> <input_name> <output_name_base>
> >
> > and two files are generated from this script: "output_name_base.fasta" and 
> > "output_name_base.txt".
> >
> > I am at a loss of how these parameter should be represented in the xml 
> > format, especially how the <outputs> <data name=""> tag should be filled, 
> > since in the <command> tag, there is only one $output.
> >
> > Any suggestions?
> >
> > thanks!
> > #GalaxyNoobie
> >
> >
> > ___________________________________________________________
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> >
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> 
> 


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