Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 49:cf5597dc7d2a draft
planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 28fc368669a17c197073f8c32f75a95941d63963-dirty
| author | pjbriggs |
|---|---|
| date | Wed, 18 Dec 2019 09:51:18 +0000 |
| parents | 04e71fda5b9c |
| children | dac038bd896d |
| files | amplicon_analysis_pipeline.py |
| diffstat | 1 files changed, 13 insertions(+), 9 deletions(-) [+] |
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--- a/amplicon_analysis_pipeline.py Tue Dec 17 09:24:17 2019 +0000 +++ b/amplicon_analysis_pipeline.py Wed Dec 18 09:51:18 2019 +0000 @@ -155,12 +155,15 @@ sample_names.append(sample_name) # Reference database - if args.use_silva: + if args.pipeline == "Vsearch": + if args.use_silva: + ref_database = "silva" + elif args.use_homd: + ref_database = "homd" + else: + ref_database = "gg" + elif args.pipeline == "DADA2": ref_database = "silva" - elif args.use_homd: - ref_database = "homd" - else: - ref_database = "gg" # Construct the pipeline command print "Amplicon analysis: constructing pipeline command" @@ -180,10 +183,11 @@ if args.reference_data_path: pipeline.add_args("-r",args.reference_data_path) pipeline.add_args("-P",args.pipeline) - if ref_database == "silva": - pipeline.add_args("-S") - elif ref_database == "homd": - pipeline.add_args("-H") + if args.pipeline == "Vsearch": + if ref_database == "silva": + pipeline.add_args("-S") + elif ref_database == "homd": + pipeline.add_args("-H") # Echo the pipeline command to stdout print "Running %s" % pipeline