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.hotz@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-bounces@lists.bx.psu.edu> <galaxy-user-bounces@lists.bx.psu.edu> wrote:
>
> >
> > From: Lifeng Lin <linlifeng@gmail.com>
> > Date: March 25, 2014 12:58:52 AM GMT+01:00
> > To: <galaxy-user@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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