Command line arguments are often case sensitive (e.g. samtools switches), but are Galaxy parameter names?
On Sat, Feb 28, 2015 at 9:11 PM, Björn Grüning email@example.com wrote:
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/galax... ___________________________________________________________ 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/
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