Update Plasmid finder (#4845)

* 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>