Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
comparison amplicon_analysis_pipeline.py @ 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 |
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| 48:04e71fda5b9c | 49:cf5597dc7d2a |
|---|---|
| 153 final_name.write("%s\n" % '\t'.join((r1,sample_name))) | 153 final_name.write("%s\n" % '\t'.join((r1,sample_name))) |
| 154 final_name.write("%s\n" % '\t'.join((r2,sample_name))) | 154 final_name.write("%s\n" % '\t'.join((r2,sample_name))) |
| 155 sample_names.append(sample_name) | 155 sample_names.append(sample_name) |
| 156 | 156 |
| 157 # Reference database | 157 # Reference database |
| 158 if args.use_silva: | 158 if args.pipeline == "Vsearch": |
| 159 if args.use_silva: | |
| 160 ref_database = "silva" | |
| 161 elif args.use_homd: | |
| 162 ref_database = "homd" | |
| 163 else: | |
| 164 ref_database = "gg" | |
| 165 elif args.pipeline == "DADA2": | |
| 159 ref_database = "silva" | 166 ref_database = "silva" |
| 160 elif args.use_homd: | |
| 161 ref_database = "homd" | |
| 162 else: | |
| 163 ref_database = "gg" | |
| 164 | 167 |
| 165 # Construct the pipeline command | 168 # Construct the pipeline command |
| 166 print "Amplicon analysis: constructing pipeline command" | 169 print "Amplicon analysis: constructing pipeline command" |
| 167 pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh") | 170 pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh") |
| 168 if args.forward_pcr_primer: | 171 if args.forward_pcr_primer: |
| 178 if args.sliding_window_length: | 181 if args.sliding_window_length: |
| 179 pipeline.add_args("-l",args.sliding_window_length) | 182 pipeline.add_args("-l",args.sliding_window_length) |
| 180 if args.reference_data_path: | 183 if args.reference_data_path: |
| 181 pipeline.add_args("-r",args.reference_data_path) | 184 pipeline.add_args("-r",args.reference_data_path) |
| 182 pipeline.add_args("-P",args.pipeline) | 185 pipeline.add_args("-P",args.pipeline) |
| 183 if ref_database == "silva": | 186 if args.pipeline == "Vsearch": |
| 184 pipeline.add_args("-S") | 187 if ref_database == "silva": |
| 185 elif ref_database == "homd": | 188 pipeline.add_args("-S") |
| 186 pipeline.add_args("-H") | 189 elif ref_database == "homd": |
| 190 pipeline.add_args("-H") | |
| 187 | 191 |
| 188 # Echo the pipeline command to stdout | 192 # Echo the pipeline command to stdout |
| 189 print "Running %s" % pipeline | 193 print "Running %s" % pipeline |
| 190 | 194 |
| 191 # Run the pipeline | 195 # Run the pipeline |