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",
the wrapper will call your script and rename/move the output.
Hope this helps,
On Mar 25, 2014, at 3:23 AM, <galaxy-user-boun...@lists.bx.psu.edu>
> 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
> 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?
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