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iracooke / protk

Proteomics Toolkit in Ruby
MIT License
12 stars 2 forks source link

x!tandem configfile option #1

Open bgruening opened 10 years ago

bgruening commented 10 years ago

Hi Ira,

I got a request to add an option to provide a configfile option to the X!Tandem wrapper. The objective is that our users have several "profiles" of using X!tandem. Do you think that feature would be a good addition? I would start changing the wrapper to show the normal mode, as of now, but the first option would be to change it to a configfile mode, where only one additional input is requested, the config XML file.

iracooke commented 10 years ago

Hi Bjorn,

That sounds perfect … some minor changes would be needed to protk as well to ensure that the configfile options are not overridden.

Cheers Ira

On 15 Mar 2014, at 1:30 am, Björn Grüning notifications@github.com wrote:

Hi Ira,

I got a request to add an option to provide a configfile option to the X!Tandem wrapper. The objective is that our users have several "profiles" of using X!tandem. Do you think that feature would be a good addition? I would start changing the wrapper to show the normal mode, as of now, but the first option would be to change it to a configfile mode, where only one additional input is requested, the config XML file.

— Reply to this email directly or view it on GitHub.

bgruening commented 10 years ago

Hi Ira,

I have changed the wrapper to use: --config $config.config_file

https://bitbucket.org/BjoernGruening/xtandem-toolshed/commits/08d3f886a493176129a2c5e43ce1817925b65054?at=default

bgruening commented 10 years ago

Oh, I see there is already --tandem-params. Isn't that parameter supposed to do exactly what I want?

iracooke commented 10 years ago

Yes ... but maybe not quite. To be honest I doubt this will work as you expect without a fair bit of change to the protk wrapper. The --tandem-params option will override the protk defaults file ... but then what will happen is pretty much every default will be overridden by the command-line default. Yuck .. so I have two sources of defaults effectively. If you allow users to put in their own config file you would still need to modify it as well to fix all the paths contained in that file .... so it's actually not that easy.

Sorry to have led you down the wrong path here. I would ask your users what they "really" need in this feature. Supporting that might be easier.

iracooke commented 10 years ago

Sorry one final point ... is that the only useful thing here that users could perhaps benefit from is anything they add to their config file that is not supported by protk will be preserved. So maybe they get some benefit there ... but the protk wrapper supports a heck of alot of x!tandem functionality.

bgruening commented 10 years ago

The idea was to provide something like a "profile" xml files, to save the time of setting every parameter again. They have 3 different settings and reuse them a lot. I'm also sceptical about such an option, because it's somehow contradicting the Galaxy Idea. Via the TPP webinterface you can provide such an paramter XML file and it only contains the paramters, the different paths will be added right before execution. Would that be possible? Also in case of Galaxy I do not the the problem of overriding the parameters, because Galaxy will not set any paramter if a config file is given (besides the input files). If that does not make much sense or is difficult to implement, I will try to convince our users to enter the parameters every time and workaround with predefined workflows.