Indeed, the 'awk' tool accepts 'format="txt"' and therefore can handle almost any file in Galaxy. Regarding your other question ('user parameters ending up on command line'), here's my suggestion: In the <command> section, enclose the parameter in single-quotes (make sure it's single and not double): <command interpreter="sh">awk_wrapper.sh $input $output '$file_data'</command> In the program parameter (where users can enter whatever they want), add a validator to prevent single-quotes: <param name="file_data" type="text" area="true" size="5x35" label="AWK Program" help=""> <validator type="expression" message="Invalid Program!">value.find('\'')==-1</validator> </param> This way the parameters the user enter will always be single-quoted, and not parsed by the shell. -Gordon. James Casbon wrote, On 11/25/2008 12:31 PM:
Great, thanks a lot. You're way ahead of me here ;)
2008/11/25 James Taylor <james.taylor@emory.edu>:
James,
The datatypes are a hierarchy, and tools will accept any type that is more specific than their defined input type. If you set the input type to "data" the tool will accept anything, if you set it to "text" it will accept any text format.
For outputs, there is a special format "input" which copies the type of the input dataset (first input I believe, this needs to be enhanced to allow specifying a particular input). There is also the "metadata_source" attribute for copying the input metadata. This is how many of our tools that work on tabular data preserve the type and metadata of "interval" format files.
-- jt
On Nov 25, 2008, at 6:14 AM, James Casbon wrote:
Is there a way to define a tool which accepts more any type of input? It should ideally preserve the format in the output as well.