[WIP]: changes that accumulate during working on checkm parsers #65
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
bernt-matthias
force-pushed
the
topic/improvements_for_checkm
branch
from
6bb1efe to
7c8f4b0
Compare
This was referenced Apr 29, 2020
bernt-matthias
force-pushed
the
topic/improvements_for_checkm
branch
6 times, most recently
from
1a20271 to
0d86bef
Compare
Collaborator
Author
|
Galaxy part seems ready. But now cwl can't cope anymore... |
hexylena
reviewed
May 14, 2020
Owner
|
looks like we might need to update the cwl example, looks fine though to use the output of tmp.cwl / tmp-sub.cwl |
bernt-matthias
force-pushed
the
topic/improvements_for_checkm
branch
2 times, most recently
from
e1decb3 to
b96d733
Compare
- implement output to dir (--directory) to output separate tool per subparser - prepare to include global macro file (for including requirements, citations, help, ...)
corresponding to hexylena/galaxyxml#18
- output to dir, diff dirs, planemo dir
since dicts (and hopefully also attributes) are ordered
- remove '.py' extension if existent - replace '-' by '_' - for id: replace ' ' by '_' also overwrite tool xml files (wo warning)
bernt-matthias
force-pushed
the
topic/improvements_for_checkm
branch
from
b96d733 to
7f6fa0c
Compare
…rnt-matthias/argparse2tool into topic/improvements_for_checkm
and test cleanup
bernt-matthias
force-pushed
the
topic/improvements_for_checkm
branch
from
7e157e2 to
b40d46e
Compare
if directory is specified.
- print error message if parameter can not be translated - cwl: implement StoreConst, Help, and Version actions - xml: implement HelpAction
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Will add commits as they come. Early feedback is welcome.