Hi Lifeng,
Another option would be the 'from_work_dir' option to the <data> tag. Have
a look at the tophat repository in the Tool Shed for an example:
http://toolshed.g2.bx.psu.edu/view/devteam/tophat
--nate
On Tue, Mar 25, 2014 at 11:29 AM, Hans-Rudolf Hotz
<hansrudolf.h...@fmi.ch>wrote:
> 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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