Re: [galaxy-dev] Looking for a running example of planemo test with options from_data_table

2018-02-15 Thread nsora...@tiscali.it 
Dear Laure,have a look at 
https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wrappers/bowtie_wrapper.xml
Cheers,Nicola
-- Messaggio originale--Da: Laure QUINTRICData: gio 15 feb 2018 16:06A: 
galaxy-dev@lists.galaxyproject.org;CC: Patrick Durand;Olivier 
Inizan;Oggetto:[galaxy-dev] Looking for a running example of planemo test with 
options from_data_table
Dear list,

Is there somewhere in the Galaxy any running example of a planemo test 
embracing a from_data_table option ?

We are trying to reproduce the picard example referenced here:
https://github.com/jmchilton/picard/commit/4df8974384081ee1bb0f97e1bb8d7f935ba09d73#diff-4145b3df5cbab370b2450e33dc343c3a

We also have a look on several examples on the IUC, unfortunately it 
seems to work only with values from history.

Many thanks,

Laure, Patrick and Olivier.
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Re: [galaxy-dev] "Edit attributes" for interval dataset not consistent with documentation

2018-01-18 Thread nsora...@tiscali.it 
Dear Peter,this bug has been recently reported in 
https://github.com/galaxyproject/galaxy/issues/4966 and fixed in 
https://github.com/galaxyproject/galaxy/pull/5027 for the upcoming 18.01 Galaxy 
release.Not sure if this is worth a backport, but if you need it for 17.09 and 
want to try, it should be feasible.
Cheers,Nicola
-- Messaggio originale--Da: Peter BriggsData: gio 18 gen 2018 12:11A: 
galaxy-dev@lists.galaxyproject.org;CC: Oggetto:[galaxy-dev] "Edit attributes" 
for interval dataset not consistent with documentation
Dear Devs

One of my local users has noticed that the "edit attributes" function for 
"interval"-type datasets is not consistent with the documentation at:

https://galaxyproject.org/learn/datatypes/#interval

This states that only CHROM, START, and END are required, with the implication 
that other fields are optional.

However when editing the attributes for a dataset, if either of "Strand" or 
"Name" are not set to an explicit column number then "Save attributes" fails 
with the message: "Error occurred while saving. Please fill all the required 
fields and try again."

This is true on both our local Galaxy running release_17.09 and also on Galaxy 
main.

Is this a bug in the documentation, or the implementation?

Thanks,

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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