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Commit Graph
19 Commits
Author SHA1 Message Date
Nicola Soranzo c2eebd0bbe Fix `'myst' cross-reference target not found` warnings 
Also:
- Use auto-generated table of contents in tool schema
 2023-03-27 15:07:21 +01:00
Matthias Bernt e52a98152a include ActionsOption in schema doc 2023-02-06 10:51:11 +01:00
Marius van den Beek 7cb3f76c6e Merge pull request #12232 from bernt-matthias/topic/drilldown 
fix `drill_down` parameters
 2022-05-25 15:52:50 +02:00
Matthias Bernt cfa1b93669 another try to fix xsd 2022-03-22 09:28:04 +01:00
Matthias Bernt c194cc62f1 fix doc for expect_num_pairs and add test tool 
also the TOC for discovered_dataset was wrong
and fixed a minor typo in comments in xsd
 2022-01-30 15:21:34 +01:00
Matthias Bernt 914818098f add doc for test/param/metadata 
currently only linking to a stub at the planemo docs
 2021-12-17 19:06:10 +01:00
John Chilton 48df4b910d Systematic handling of remotely required tool files. 
- Allow tools to define "pulsar file action"-like paths for files to include and exclude during remote job setup.
- Package up a list of defaults for older tools.
 2021-08-10 14:04:32 -04:00
Martin Cech 2c0a60d801 add <creator> to the schema template, use live links in xsd 2021-07-09 18:28:15 +02:00
ValentinMarcon 94328b9684 merge dev into toolref 2019-06-24 15:03:12 +02:00
John Chilton 41f6584e6f Refactor XSD output elements to share output attributes. 2019-03-18 15:06:48 -04:00
mvdbeek 5e098857e5 Display test collection input in documentation 2018-11-07 20:08:21 +01:00
Nicola Soranzo 59c1ed2266 Various doc fixes 2018-09-03 14:34:13 +01:00
Nicola Soranzo 08cb278cc9 Add various elements to the Tool XML doc page 
In particular:
- macros
- edam_topics
- edam_operations
- environment_variables and subelement
- request_param_translation and subelements

Also:
- reorder elements to follow IUC coding style
- in examples:
  - use lowercase ``true`` and ``false`` for boolean attributes
  - add/use single quotes
- minor doc fixes
 2017-10-26 15:43:12 +01:00
John Chilton 074e10ac00 Fix tool XSD to document <conversion> tag for data parameters. 
Rebased with English fixes and small tool cleanups thanks to @nsoranzo.
 2017-01-20 13:05:42 -05:00
Nicola Soranzo 3180b63166 Properly integrate tool XML schema with docs 
Generate intermediate rst file instead of html
Move generation to doc/Makefile
Use pandoc to generate table of contents and fragment ids.
Remove nested inline markup (not supported by reStructuredText)
Fix https and other links.
 2016-10-24 19:42:19 +01:00
Martin Cech 7eb413f4e8 Merge pull request #2961 from jmchilton/xsd_fixes_1 
Improve ``version_command`` tag.
 2016-10-17 13:31:52 -04:00
Martin Cech 750cb7c584 encourage bug reporting in tool schema 2016-09-26 12:52:52 -04:00
John Chilton e8f35310ba Revise and improve `version_command` tag. 
- Include deprecated ``interpreter`` tag in XSD. (Closes galaxyproject/planemo#574)
- Allow the use of ``$__tool_directory__`` in interpreter command (so we can actually call ``interpreter`` deprecated).
- Include sample tools of both of these styles.
- General improvements to the version command documentation.
 2016-09-23 13:31:07 -04:00
John Chilton a8bc9d5d16 XSD Generated Tool Documentation. 
- Add script to generate Markdown documentation from the XSD.
 - Add Makefile target to build these docs, convert to HTML, and open respectively.
 2016-09-21 08:41:12 -04:00