Hi,
I am working on a wrapper that has multiple combinations of switches that lead to the creation of the output files. For instance, one of the files can be generated by conditions "A and B" and also by "A and C". FIrst, I tried the xml <and> and <or> elements, but that didn't work. Next, I tried having two <data> elements with the same name that contained those two pairs of filters. However, it appears that Galaxy only checks the last <data> element, which in this case is "A and C", so "A and B" is never triggered. In other cases there are three variables in play as the two main variables are not initialized if the advanced options conditional parameter's value is on. Passing the options to the wrapper is not a problem - only setting the outputs.
I pasted the complete tool definition file at http://pastebin.com/BGDzcc28.
Thanks,
Alex