Re: [galaxy-dev] Tool wrapper XSD

>> Is there a Galaxy XML tool wrapper XSD ? > I worked more on this XSD. It now passes 181 (and fails on 163) of the 352 tools packaged in galaxy-dist − it starts being somehow useful. > Many wrappers also use constructs which are not yet documented on th

Re: [galaxy-dev] Tool wrapper XSD

Hi, > > If you are going to write one and want a starting point, here is > > the schema I used Thanks John for sharing your XSD. I forked and started to complete it at: I worked on it until my own tool wrapper passed, but it needs more work for any oth

[galaxy-dev] Deploying LOC files for tool built-in data during a tool installation

Hi list, The tool I am currently wrapping has built-in data, which may be used by the tool users (through a relevant < from_data_table> + .LOC file configuration). They are .fasta databases which are rather small and are thus bundled in the tool distribution package. Thanks to the tool_depen

[galaxy-dev] Behaviour of download_by_url with tar.gz during tool dependency installation

Hi list, When working to get a tool wrapper Toolshed-ready, I have explored how tool dependencies installation works, especially the download_by_url feature. I have summarised my understanding on the Wiki (hope this is clear and accurate):

Re: [galaxy-dev] Questions about tool wrapping

> >> Unfortunately, I can't help much with refresh_on_change either, we just > >> use the / tag set. I have been under the impression > >> the the documentation has been written for 'refresh_on_change' in the > >> meantime. I am sorry, I should have checked first, before suggesting it. > > > > No

Re: [galaxy-dev] Questions about tool wrapping

> Unfortunately, I can't help much with refresh_on_change either, we just > use the / tag set. I have been under the impression > the the documentation has been written for 'refresh_on_change' in the > meantime. I am sorry, I should have checked first, before suggesting it. No problem. I’ll know

Re: [galaxy-dev] Questions about tool wrapping

Hi Hans-Rudolf, Thank you for your answer. > > I am not sure of the best design here. > > *Providing another wrapperfor this other binary, with users > > explicitly > > using it beforehand in their workflow? > > *Assuming the databases have been processed outside of Galaxy > > beforehand > > ? (A

[galaxy-dev] Questions about tool wrapping

Hi list, I am currently writing a Galaxy wrapper (for SortMeRNA [1]) and I would have several questions. == Pre-processing an input == SortMeRNA filters rRNA reads against an indexed rRNA database. This database can either be one bundled together with SortMeRNA and defined in a relevant .