[galaxy-dev] Components

[Mariette]

Thanks for the answer,
Still considering the number of outputed files problem. In my script I 
know that if
a cleaning option is set 2 other files will be created, so I check if 
the option is asked by the
user and try this :

  <outputs>
    <data name="log" format="txt" />
    #if $clean_pairends.clean_pairends_select=="y":
        <data name="output" format="input"/>
    #end if
  </outputs>

but this is not working ... there is a way to do what I want ?
thx
Jerome




Peter Cock a écrit :
> On Tue, Jun 7, 2011 at 9:24 AM, Mariette <jmariett at toulouse.inra.fr> wrote:
>   
>> Thanks for the answer,
>>
>> so I tryed to write a wrapper, but the main script is not recognize.
>> When I'm calling my wrapper in the xml file, I don't have to specify
>> the full path but then from my wrapper if I want to call my main script
>> I can't if this one is not on the PATH ? the wrapper current directory
>> is the job_working_directory, there is anyway to access my main script
>> just like it's done for the wrapper ?
>>     
>
> Generally put the wrapper script next to your tool XML file, and don't
> prefix it with any path in the <command> tag in the XML, e.g.
>
> /opt/galaxy/tools/mariette/my_tool.xml
> /opt/galaxy/tools/mariette/my_tool.sh
>
> (or my_tool.py or my_tool.pl etc depending on what language you used)
>
> Your wrapper script then has to call the real executable, and the
> normal way to do this on Unix is to have it on the PATH. You could
> also hard code an absolute path.
>
> Peter
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