Thanks Dannon! This was exactly what I was looking for! 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.
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