On Tue, Dec 13, 2011 at 7:29 PM, Dannon Baker <dannonbaker@me.com> wrote:

Roger,

The <repeat> construct creates an array of the various inputs over which you can iterate within the command template of your tool config. See the concatenate datasets wrapper (tools/filters/catWrapper.xml) for a full example, but here are the relevant sections inline:

<repeat name="queries" title="Dataset">
<param name="input2" type="data" label="Select" />
</repeat>

<command interpreter="python">
catWrapper.py
$out_file1
$input1
#for $q in $queries
${q.input2}
#end for
</command>

-Dannon

On Dec 13, 2011, at 9:47 PM, Roger Ngo wrote:

> Hello all,
>
> I have a question on how the <repeat> tag works in a Galaxy tool XML file.
>
> Right now I have a perl script that takes in various arguments. One of the arguments I have is a repeated one which is just a file selection feature.
>
> The script works something like this:
>
> script.pl $arg1 $arg2 $varyingNumOfArgs
>
> By using <repeat>, is the execution of the script something like this?
>
> script.pl $arg1 $arg2 $repeatedArg1 $repeatedArg2 ... $repeatedArgN
>
> where repeatedArgs1 ... repeatedArgsN are basically arguments specified by the <repeat> tag.
>
> If so, is there a certain way to access these repeated arguments and pass them into my script in the <command> tag? This is the part where I am not quite sure how <repeat> works.
>
> Thanks

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