Indeed, the 'awk' tool accepts 'format="txt"' and therefore can
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
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"
label="AWK Program" help="">
This way the parameters the user enter will always be single-quoted, and
not parsed by the shell.
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(a)emory.edu>:
> 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
> 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
> 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
> -- 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.