[emboss-dev] Commandline changes in EMBOSS applications

Peter Rice pmr at ebi.ac.uk
Thu Sep 29 15:20:24 UTC 2011

On 09/29/2011 04:03 PM, Peter Cock wrote:
> On Thu, Sep 29, 2011 at 3:43 PM, Peter Rice<pmr at ebi.ac.uk>  wrote:
>> A question for our developer community...
>> I am working through the GALAXY wrappers for EMBOSS applications. GALAXY has
>> a very clean way to define command line applications which is close to
>> EMBOSS's ACD definitions, so most applications are easy to define.
>> I have problems where the default values in the ACD file depend on other
>> values. Two examples from prettyplot illustrate the problem. In both cases,
>> the current GALAXY definitions ignore these qualifiers.

> In theory you can use an optional integer parameter in Galaxy,
> with an empty default,  meaning the user doesn't have to put in
> a value. You can then check this in the tool wrapper's XML
> <command>  tag with Cheetah syntax to decide if you add
> the -switch value to the command string (with the user's value),
> or not (to get the EMBOSS default).

Thanks for the tip. I found the GALAXY documentation on this at 

So, possible in GALAXY but these ACD files are an issue for other 
wrapper developers. Therefore I would still like to replace them as far 
as possible.

The GALAXY conditionals would be very useful for the phylipnew EMBASSY 
package where qualifiers depend on a set of selection menus... but I am 
not planning to add those applications just yet ... unless there is a 
demand for them, of course.


Peter Rice

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