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 > > > ___________________________________________________________ > 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
