On Fri, Feb 15, 2013 at 4:32 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>>>> Usecase: Tool comes with a simple datafile (e.g. defining a search motif,
>>>> say motif.dat) which is used by a script (say motif.py) via a normal
>>>> Galaxy tool XML file (say motif.xml).
>>>> Perhaps I can just put my data file next to the script and XML file, in
>>>> which case it is easy for the script to locate? But I assumed that
>>>> Galaxy best practice would be to use the tool-data folder somehow...
>>>> Thanks,
>>>> Peter
>> Is there a documented example I should be reading? In this use case
>> (without any explicit XML markup), can I assume/have the motif.dat
>> file be installed in the same folder next to the motif.py script and tool
>> defining motif.xml file?
> This scenario uses a tool dependency that is included in the repository
> which is discussed in the following section of the tool shed wiki.  Using
> this approach a tool config (Cheetah template) would have to be
> configured with the proper <requirement> tag set and an associated
> <command> tag set that would ultimately have the path to the motif.py
> script and motif.dat file defined in the environment.  Of course, this
> assumes the motify.py script is not the tool executable itself.

Actually for the example I am working on, the motif.py script would be
the tool executable, called from motif.xml like this:

<command interpreter="python">motif.py $fasta_file $tabular_file</command>

i.e. A completely self contained Galaxy tool consisting of four files:

motif.xml - Galaxy tool definition
motif.txt - README file
motif.py - Python script which is the tool
motif.dat - Data file used by the Python script

I am hoping that no further XML configuration files are needed in
order to handle the data file.

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