Am 04.03.2015 um 02:37 schrieb John Chilton: > 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.
I think so too, never tried it but I guess they are case sensitive and no '-' is allowed. > Bjoern, > > Is this what you mean? > > https://github.com/galaxyproject/galaxy/compare/dev...jmchilton:argument_name?expand=1 Pretty much yes! > If it is what you want - I can open a pull request for it. I was posting it here to get a small discussion started. If there are no complains and every one is happy, please do so :) > 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? Can you elaborate here a little bit more? My point is that the actual parameter _is_ important to map against the original tool documentation, some pdfs etc. It's also important to map some paper's method section back to a Galaxy tool. So I think it should be available for the user. Currently, best practise is to put it into help. This is good, but clutters the UI and it is unstructured. Unstructured in a way, so that I can not easily get it, for example via the API. If we have this information as extra attribute we display it in a special way in the new JS tool form, independent from the help text. And I could get this information to do nasty things on a potential GalaxyShell with it. > 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). Which abstraction do we break? Do you have an example? I think in most of the cases a param maps one-to-one to an argument, isn't? (There are special cases, but this does not go away and need to stay.) I think this attribute is just an additional way to structure our params and make it easier to map and document them. Thanks, this kind of discussion I wanted to have :) Cheers, Bjoern > -John > > > On Tue, Mar 3, 2015 at 11:38 AM, Peter Cock <p.j.a.c...@googlemail.com> 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.gruen...@gmail.com> 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 . >>> >>> 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 >>> >>>  >>> https://github.com/claresloggett/gvl_commandline_utilities/blob/master/galaxy-fuse.py >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. 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