Mercurial > repos > pjbriggs > amplicon_analysis_pipeline
changeset 1:1c1902e12caf draft
Updated to version 1.2.1.0
| author | pjbriggs |
|---|---|
| date | Wed, 25 Apr 2018 03:54:00 -0400 |
| parents | 47ec9c6f44b8 |
| children | 43d6f81bc667 |
| files | README.rst amplicon_analysis_pipeline.py amplicon_analysis_pipeline.xml install_tool_deps.sh |
| diffstat | 4 files changed, 30 insertions(+), 10 deletions(-) [+] |
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--- a/README.rst Thu Nov 09 10:13:29 2017 -0500 +++ b/README.rst Wed Apr 25 03:54:00 2018 -0400 @@ -218,6 +218,9 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +1.2.1.0 Updated to Amplicon_Analysis_Pipeline version 1.2.1 (adds + option to use the Human Oral Microbiome Database v15.1, and + updates SILVA database to v123) 1.1.0 First official version on Galaxy toolshed. 1.0.6 Expand inline documentation to provide detailed usage guidance. 1.0.5 Updates including:
--- a/amplicon_analysis_pipeline.py Thu Nov 09 10:13:29 2017 -0500 +++ b/amplicon_analysis_pipeline.py Wed Apr 25 03:54:00 2018 -0400 @@ -120,6 +120,7 @@ type=str.lower, default="vsearch") p.add_argument("-S",dest="use_silva",action="store_true") + p.add_argument("-H",dest="use_homd",action="store_true") p.add_argument("-r",dest="reference_data_path") p.add_argument("-c",dest="categories_file") args = p.parse_args() @@ -150,6 +151,14 @@ final_name.write("%s\n" % '\t'.join((r2,sample_name))) sample_names.append(sample_name) + # Reference database + if args.use_silva: + ref_database = "silva" + elif args.use_homd: + ref_database = "homd" + else: + ref_database = "gg" + # Construct the pipeline command print "Amplicon analysis: constructing pipeline command" pipeline = PipelineCmd("Amplicon_analysis_pipeline.sh") @@ -168,8 +177,10 @@ if args.reference_data_path: pipeline.add_args("-r",args.reference_data_path) pipeline.add_args("-P",args.pipeline) - if args.use_silva: + 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 @@ -190,6 +201,7 @@ except Exception as ex: # Some other problem sys.stderr.write("Unexpected error: %s\n" % str(ex)) + exit_code = 1 # Write out the list of outputs outputs_file = "Pipeline_outputs.txt" @@ -298,8 +310,7 @@ boxplots_dir = os.path.abspath( os.path.join("RESULTS", "%s_%s" % (args.pipeline.title(), - ("gg" if not args.use_silva - else "silva")), + ref_database), "Alpha_diversity", "Alpha_diversity_boxplot", "Categories_shannon"))
--- a/amplicon_analysis_pipeline.xml Thu Nov 09 10:13:29 2017 -0500 +++ b/amplicon_analysis_pipeline.xml Wed Apr 25 03:54:00 2018 -0400 @@ -1,7 +1,7 @@ -<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.0.6"> +<tool id="amplicon_analysis_pipeline" name="Amplicon Analysis Pipeline" version="1.2.1.0"> <description>analyse 16S rRNA data from Illumina Miseq paired-end reads</description> <requirements> - <requirement type="package" version="1.1">amplicon_analysis_pipeline</requirement> + <requirement type="package" version="1.2.1">amplicon_analysis_pipeline</requirement> <requirement type="package" version="1.11">cutadapt</requirement> <requirement type="package" version="1.33">sickle</requirement> <requirement type="package" version="27-08-2013">bioawk</requirement> @@ -22,10 +22,12 @@ </stdio> <command><![CDATA[ ## Set the reference database name - #if $reference_database == "" + #if $reference_database == "-S" + #set reference_database_name = "silva" + #else if $reference_database == "-H" + #set reference_database_name = "homd" + #else #set reference_database_name = "gg" - #else - #set reference_database_name = "silva" #end if ## Run the amplicon analysis pipeline wrapper @@ -52,7 +54,7 @@ -P $pipeline -r \$AMPLICON_ANALYSIS_REF_DATA_PATH #if str( $reference_database ) != "" - "${reference_database}" + ${reference_database} #end if #if str($categories_file_in) != 'None' -c "${categories_file_in}" @@ -186,6 +188,7 @@ label="Reference database"> <option value="" selected="true">GreenGenes</option> <option value="-S">Silva</option> + <option value="-H">Human Oral Microbiome Database (HOMD)</option> </param> </inputs> <outputs>
--- a/install_tool_deps.sh Thu Nov 09 10:13:29 2017 -0500 +++ b/install_tool_deps.sh Wed Apr 25 03:54:00 2018 -0400 @@ -35,6 +35,9 @@ rm -rf $wd/* rmdir $wd } +function install_amplicon_analysis_pipeline_1_2_1() { + install_amplicon_analysis_pipeline $1 1.2.1 +} function install_amplicon_analysis_pipeline_1_1() { install_amplicon_analysis_pipeline $1 1.1 } @@ -686,7 +689,7 @@ mkdir -p $TOP_DIR fi # Install dependencies -install_amplicon_analysis_pipeline_1_1 $TOP_DIR +install_amplicon_analysis_pipeline_1_2_1 $TOP_DIR install_cutadapt_1_11 $TOP_DIR install_sickle_1_33 $TOP_DIR install_bioawk_27_08_2013 $TOP_DIR