On Feb 15, 2013, at 11:45 AM, Peter Cock wrote:

> 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.
> 
> Peter

In this case, your motif.xml file can be configured with the following:

<command interpreter="python">
    motif.py $fasta_file $tabular_file
</command>
<requirements>
    <requirement type="set_environment">MOTIF_DAT_PATH</requirement>
</requirements>

and your repository will need to include the following tool_dependencies.xml 
file:

<?xml version="1.0"?>
<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="MOTIF_DAT_PATH" 
action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
</tool_dependency>





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