Am 04.03.2015 um 02:37 schrieb John Chilton:
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.
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
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
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 :)
On Tue, Mar 3, 2015 at 11:38 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
> Hi Björn,
> Command line arguments are often case sensitive
> (e.g. samtools switches), but are Galaxy parameter
> On Sat, Feb 28, 2015 at 9:11 PM, Björn Grüning
> <bjoern.gruening(a)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
>> 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!
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