obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

obi export: added options to export to metabaR compatible format

Browse Source
This commit is contained in:
mercierc
2021-11-11 15:24:12 +13:00
parent 5a8b9dca5d
commit f6353fbf28
5 changed files with 127 additions and 7 deletions
Download Patch File Download Diff File Expand all files Collapse all files

23
python/obitools3/apps/optiongroups/__init__.py
View File

@ -297,6 +297,29 @@ def __addExportOutputOption(optionManager):
const=b'tabular',
help="Output file is in tabular format")
group.add_argument('--metabaR-output',
action="store_const", dest="obi:outputformat",
default=None,
const=b'metabaR',
help="Export the files needed by the obifiles_to_metabarlist function of the metabaR package")
group.add_argument('--metabaR-prefix',
action="store", dest="obi:metabarprefix",
type=str,
help="Prefix for the files when using --metabaR-output option")
group.add_argument('--metabaR-ngsfilter',
action="store", dest="obi:metabarngsfilter",
type=str,
default=None,
help="URI to the ngsfilter view when using --metabaR-output option (if not provided, it is not exported)")
group.add_argument('--metabaR-samples',
action="store", dest="obi:metabarsamples",
type=str,
default=None,
help="URI to the sample metadata view when using --metabaR-output option (if not provided, it is built as just a list of the sample names)")
group.add_argument('--only-keys',
action="append", dest="obi:only_keys",
type=str,