[galaxy-dev] Boolean options in toolconfigs: yes/no vs. give/omit flag.

[Samuel Lampa]

On 08/23/2011 03:47 AM, Peter Cock wrote:
> On Mon, Aug 22, 2011 at 5:29 PM, Samuel Lampa
> <samuel.lampa at 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

Many thanks for this info, that helps a lot!

I guess I will either need to parse the cheetah if-syntax then (have 
actually played with a rudimental parser in ANTLR already[1]) or just do 
some modifications of the tool config files, to make them work for our 
purposes [2]. Any other hints are of course welcome!

Cheers,
Samuel

[1] 
http://saml.rilspace.org/ebnf-parser-for-parts-of-the-galaxy-toolconfigs-with-antlr
[2] Basically we have been prepared to need to do this anyway, since we 
cannot make use of wrappers using an accompanying script file, but we 
have assumed that the existing tool configs will be much valuable as a 
starting point anyway.


-- 
System Expert / Bioinformatician
SNIC-UPPMAX HPC Center
Uppsala University, Sweden
--------------------------------------
E-mail: samuel.lampa at scilifelab.uu.se
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