Hi Matthias,
If you look at the HTML composite datatype, there is a master file (HTML),
and an arbitrary number of arbitrarily named child files like images.
The BLAST database datatype follows this, but we have used a simple
text file as the master file (just the stdout from makeblastdb) in orde
Hi,
thanks for your support. This helps.
I have thought a bit about composite data types. And have additional
questions.
In my case the additional data is essentially a folder (w subfolders).
The contents of the folder vary (it depends on the input of the programs
that generate them). So th
This is probably a John Chilton question, as the Planemo lead.
The way I do it is to "manually" install the datatype into a Galaxy
test instance (adding entries to the datatypes_conf.xml and Python
files to Galaxy's internal library), and then call ``planemo test``
pointing at this test instance.
Dear Peter,
you are right. I hope that this will be much less in the end (I'm still
learning about the package).
The main question still remains, how do I get `planemo test` to include the
data types defined in the xml file?
Best,
Matthias
Am 16/08/18 18:32 schrieb Peter Cock :
>
Defining 20 different text-based formats does not look ideal (if that
is what you are doing).
Do you have sample output in the repository? Perhaps at least some of
these can be better defined as tabular instead?
Or, perhaps you can define one composite datatype for the folder of
output instead?
Hi Peter,
I hope that subclassing simple data types will be sufficient.
More details:
I'm currently trying to (auto)wrap the checkm suite
https://github.com/Ecogenomics/CheckM. Current state here:
https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/checkm.
These tools often
More details might help - are you just defining the new datatype as a
subclass in the XML, or do you need to include Python code (e.g. for a
sniffer)?
If you want to see some examples of datatypes using Python code which
are available via the Tool Shed, here are two:
https://github.com/peterjc/ga
Dear list,
just a request for links to documentation: How can I realize tool
specific data types. I'm just developing a set of tools that need their
own data types, but I don't want to add them to Galaxy's core data types
(yet).
I've seen examples of tools that had a datatypes_conf.xml. So I
