Bakta update to 1.5.0 #4787
Merged
Bakta update to 1.5.0 #4787
Conversation
This file contains 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
Add a checkbox for output selection list Add a new test for the checkboxes
|
You need a rebase here @pimarin |
Add a checkbox for output selection list Add a new test for the checkboxes
bgruening
reviewed
Sep 16, 2022
bgruening
approved these changes
Sep 16, 2022
bgruening
added a commit
that referenced
this pull request
Oct 14, 2022
* rebuild test for summary
* add the html summary output as a one html file with all the sample outputs
* update version tool
* update test log files
* change version of the update, test files, and indentation
* update test file for the 4 test
* PR for shovill and bam files
* update from comments
* update test data and xml file for element identifier and re lib
* update log diff for test 4 and add {} for identifier and extension file
* restore &&
* ok
* restore test 4
* remove the edam section
* remove the echo test and corrige the if test
* update logfile option
* in progress
* change filter option for bam file
* new tool isescan
* first draft of isescan
* line_diff
* diff line
* failed to extract output files
* add a symlink to retrieve all output files
* fix number of output and filter for the logfile
* fix the logfile test
* Update isescan.xml
* not finished to fix all remarks
* update test
* resolve some indentation error
* proper information for bam file
* add a lines_diff for bam file
* check test 7
* try solve error in bam file
* test bam file using size estimation
* PR for shovill and bam files
* ok
* restore test 4
* remove the edam section
* in progress
* change filter option for bam file
* not finished to fix all remarks
* update test
* resolve some indentation error
* proper information for bam file
* add a lines_diff for bam file
* check test 7
* try solve error in bam file
* test bam file using size estimation
* first draft of isescan
* line_diff
* diff line
* failed to extract output files
* add a symlink to retrieve all output files
* remove shovill.bam
* PR for shovill and bam files
* ok
* restore test 4
* remove the edam section
* in progress
* change filter option for bam file
* not finished to fix all remarks
* update test
* resolve some indentation error
* proper information for bam file
* add a lines_diff for bam file
* check test 7
* try solve error in bam file
* test bam file using size estimation
* remove shovill.bam
* Bakta update to 1.5.0 (#4787)
* add a new tool BAKTA for genome annotation
* update bad indentation in shed.yml
* change file for size test
* remove a F letter added by mistake
* Add a checkbox for skip options
Add a checkbox for output selection list
Add a new test for the checkboxes
* change the help text format and change the regex
* add validator for organism level
* add regex and help
* fix in the help part
* update bakta version from 1.4.2 to 1.5.0 and change the galaxy tool version
* rebase
* change file for size test
* Add a checkbox for skip options
Add a checkbox for output selection list
Add a new test for the checkboxes
* add regex and help
* fix in the help part
* update bakta version from 1.4.2 to 1.5.0 and change the galaxy tool version
* rebase and update to 1.5.0
* restore 0 version
* Add HAPO-G: assembly polishing (#4786)
* Add HAPO-G: assembly polishing
* reorder param tag
* update to 1.3.3
* restore the isescan
* not working with docker
* remove the format file
* increase version
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
bgruening
added a commit
that referenced
this pull request
Oct 14, 2022
* rebuild test for summary
* add the html summary output as a one html file with all the sample outputs
* update version tool
* update test log files
* change version of the update, test files, and indentation
* update test file for the 4 test
* PR for shovill and bam files
* update from comments
* update test data and xml file for element identifier and re lib
* update log diff for test 4 and add {} for identifier and extension file
* restore &&
* ok
* restore test 4
* remove the edam section
* remove the echo test and corrige the if test
* update logfile option
* in progress
* change filter option for bam file
* new tool isescan
* first draft of isescan
* line_diff
* diff line
* failed to extract output files
* add a symlink to retrieve all output files
* fix number of output and filter for the logfile
* fix the logfile test
* Update isescan.xml
* not finished to fix all remarks
* update test
* resolve some indentation error
* proper information for bam file
* add a lines_diff for bam file
* check test 7
* try solve error in bam file
* test bam file using size estimation
* PR for shovill and bam files
* ok
* restore test 4
* remove the edam section
* in progress
* change filter option for bam file
* not finished to fix all remarks
* update test
* resolve some indentation error
* proper information for bam file
* add a lines_diff for bam file
* check test 7
* try solve error in bam file
* test bam file using size estimation
* first draft of isescan
* line_diff
* diff line
* failed to extract output files
* add a symlink to retrieve all output files
* remove shovill.bam
* PR for shovill and bam files
* ok
* restore test 4
* remove the edam section
* in progress
* change filter option for bam file
* not finished to fix all remarks
* update test
* resolve some indentation error
* proper information for bam file
* add a lines_diff for bam file
* check test 7
* try solve error in bam file
* test bam file using size estimation
* remove shovill.bam
* Bakta update to 1.5.0 (#4787)
* add a new tool BAKTA for genome annotation
* update bad indentation in shed.yml
* change file for size test
* remove a F letter added by mistake
* Add a checkbox for skip options
Add a checkbox for output selection list
Add a new test for the checkboxes
* change the help text format and change the regex
* add validator for organism level
* add regex and help
* fix in the help part
* update bakta version from 1.4.2 to 1.5.0 and change the galaxy tool version
* rebase
* change file for size test
* Add a checkbox for skip options
Add a checkbox for output selection list
Add a new test for the checkboxes
* add regex and help
* fix in the help part
* update bakta version from 1.4.2 to 1.5.0 and change the galaxy tool version
* rebase and update to 1.5.0
* restore 0 version
* Add HAPO-G: assembly polishing (#4786)
* Add HAPO-G: assembly polishing
* reorder param tag
* update to 1.3.3
* restore the isescan
* not working with docker
* remove the format file
* increase version
* rename the plasmidfinder_db.loc
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Anthony Bretaudeau <anthony.bretaudeau@inria.fr>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
FOR CONTRIBUTOR: