Hi all, we are planning to work on a project to implement a Galaxy fuse based shell. Probably starting with the work from Clare [1]. Next to our Galaxy IPython integration it should attract more bioinformaticians and should offer a new way to interact with Galaxy. This includes moving, deleting datasets, but also executing tools and workflows. For the latter I would like to have some sort of bash auto-completion. Type in your tool/workflow and you will see all the parameters you can/should modify, in addition to your normal help page. Currently the parameter identifiers (<param name="foo">) do not need to be meaningful. In fact many tools invent their own unique names, to identify a parameter in the cheetah section. This name is always unique but it's hard to guess it's meaning from just the name and are also not mappable to the original parameter name. This makes tool execution from the API sometimes hard. I would like to propose a new attribute for all <param> tags. This should specify a unique value that 100% matches the original parameter name of the underlying tool. This attribute could be used to: * automatically enhance the help text of each parameter. Currently best practise it to include this parameter in brackets at the end of each help text. We can do this now automatically, or only show it by mouse over etc ... * In a Galaxy shell, the user could just type in a normal command (-i history1/foo.bam -o history1/bar.sam) and Galaxy shell would be able to map this parameter to the correct <param> tag in Galaxy I greatly appreciate any comments! Thanks, Bjoern [1] https://github.com/claresloggett/gvl_commandline_utilities/blob/master/ga... ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

Peter, Galaxy parameters should be case sensitive I think - they are used in plain dictionaries quite a bit and I have never seen any logic to make them not case sensitive.

Bjoern, Is this what you mean? https://github.com/galaxyproject/galaxy/compare/dev...jmchilton:argument_...

If it is what you want - I can open a pull request for it.

I guess I am a little skeptical this is useful. I would like to believe that Galaxy tool for the most part don't need to map to a single application underneath, but we don't have to rehash that argument. If the parameter name and help is not more useful than the underlying tool's parameter - why would the tool author change it in the first place?

Jen tells me the parameter name is important, you tell me the parameter name is important, etc... I respect you guys greatly and so I will defer to you - but it is frustrating we are breaking abstractions that the tool author set up (presumably for a reason).

-John On Tue, Mar 3, 2015 at 11:38 AM, Peter Cock <p.j.a.cock(a)googlemail.com&gt; wrote: > Hi Björn, > > Command line arguments are often case sensitive > (e.g. samtools switches), but are Galaxy parameter > names? > > Peter > > On Sat, Feb 28, 2015 at 9:11 PM, Björn Grüning > <bjoern.gruening(a)gmail.com&gt; wrote: >> Hi all, >> >> we are planning to work on a project to implement a Galaxy fuse based >> shell. Probably starting with the work from Clare [1]. >> >> Next to our Galaxy IPython integration it should attract >> more bioinformaticians and should offer a new way to interact with >> Galaxy. This includes moving, deleting datasets, but also executing >> tools and workflows. For the latter I would like to have some sort of >> bash auto-completion. Type in your tool/workflow and you will see all >> the parameters you can/should modify, in addition to your normal help page. >> >> Currently the parameter identifiers (<param name="foo">) do not need to >> be meaningful. In fact many tools invent their own unique names, to >> identify a parameter in the cheetah section. This name is always unique >> but it's hard to guess it's meaning from just the name and are also not >> mappable to the original parameter name. This makes tool execution from >> the API sometimes hard. >> >> I would like to propose a new attribute for all <param> tags. This >> should specify a unique value that 100% matches the original parameter >> name of the underlying tool. >> >> This attribute could be used to: >> * automatically enhance the help text of each parameter. Currently best >> practise it to include this parameter in brackets at the end of each >> help text. We can do this now automatically, or only show it by mouse >> over etc ... >> * In a Galaxy shell, the user could just type in a normal command (-i >> history1/foo.bam -o history1/bar.sam) and Galaxy shell would be able >> to map this parameter to the correct <param> tag in Galaxy >> >> I greatly appreciate any comments! >> Thanks, >> Bjoern >> >> [1] >> https://github.com/claresloggett/gvl_commandline_utilities/blob/master/ga... >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/