Question: Creating a sub-format of Tabular with dynamic column naming
0
gravatar for joanna
2.6 years ago by
joanna70
United Kingdom
joanna70 wrote:

Please can you help us create a sub-format of Tabular that can take column headers from a specified line (perhaps denotes by “#”)? As we do not currently understand the syntax for the class definition in the python script, we’d like to check with you that it is possible before investing a lot of time into it.

In an informal chat with one of your team, as well as reading old posts with a similar probelm to solve, we were advised that creating a sub-format is the way forward, although I have not seen evidence that this was followed to completion. Could you please give us an example of code for a format definition where column headers are defined dynamically by a commented line? Or show us where the documentation for the appropriate syntax can be found?

In addition, this format would have to be able to handle a varying range of column numbers. And error handling for the absence of this header line.

Would you like more information, or would you advise that creating such a sub-format is not currently possible?

Kind regards

galaxy • 561 views
ADD COMMENTlink modified 2.6 years ago by Bjoern Gruening5.1k • written 2.6 years ago by joanna70
0
gravatar for Bjoern Gruening
2.6 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi,

this should be possible with the the latest Galaxy:dev release or Galaxy 16.04. Have a look at this PR: https://github.com/galaxyproject/galaxy/pull/961

And this tool is using it already: https://github.com/galaxyproject/tools-iuc/pull/588

Cheers, Bjoern

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Bjoern Gruening5.1k

Hi Bjoern,

Thank you so much, that's excellent news. I really appreciate this. Could you please send again the tool that uses this? The above link is a duplicate of the first. I'll see if I can get this to work and let you know.

Best wishes, Joanna

ADD REPLYlink written 2.6 years ago by joanna70

Hi, I changed the link above. Sorry.

ADD REPLYlink written 2.6 years ago by Bjoern Gruening5.1k

One more question... I often use a loc file to generate a run of interdependant select menus, the column headers of the output can vary depending on those selections. If the column names are being defined before the tool is run, is there are way to use the from_file option within this action to select the column headers based on the select options?

Many thanks

ADD REPLYlink written 2.6 years ago by joanna70

Puh, this I didn't know. I think you could use a select (and with this also a select with from_file), but this you need to try. If it works, could you please post here an example or even better submit your Tool to the IUC repo :)

Thanks! Bjoern

ADD REPLYlink written 2.6 years ago by Bjoern Gruening5.1k
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