On Mon, Aug 22, 2011 at 5:29 PM, Samuel Lampa <samuel.lampa@scilifelab.uu.se> wrote:
Hi,
I'm trying to parse the XML toolconfig format, for generating a lightweight command config wizard in an Eclipse based product.
I wonder: Boolean parameters for some tools (such as the emboss/textsearch one), seems to allow always giving the parameter's flag at all times, and just change the following value between "yes" and "no" for these params, like:
textsearch -caseinsensitive yes or textsearch -caseinsensitive no
On the other hand, I guess there are many tools which tell such boolean options just by giving the flag itself, so it would by analogy be:
textsearch -caseinsensitive or textsearch
My question is, how can I see the difference between these two cases, in the tool config file? (Unfortunately I don't know any of the wrapped tools good enough to know where to look for a flag of the latter kind).
That will be hard - there are several ways to write such a wrapper in Galaxy. e.g. a select showing the user text like "Case sensitive" and "Case insensitive" with values "yes" and "no" where the cheetah template contains: textsearch -caseinsensitive $case Or, a boolean select where the values are again "yes" and "no" with the same template. See for example "ntoa" in the BowTie wrapper, file: tools/sr_mapping/bowtie_wrapper.xml If the Unix tool expected a switch (present/absent) rather than an argument with a value (yes/no) then you might use a select with two options "Case sensitive" and "Case insensitive" with values "yes" and "no" where the cheetah template contains: textsearch #if $case=="yes" -caseinsensitive #end if Or, you might prefer to use values of "-caseinsensitive" and "" then the cheetah becomes just: textsearch $case Again, the above hypothetical select parameter $case could be a boolean parameter. e.g. See the "filter_query" option in the blastn wrapper, file tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Peter