diff --git a/q2_picrust2/_full_pipeline.py b/q2_picrust2/_full_pipeline.py index 468b8b9..8c010ee 100644 --- a/q2_picrust2/_full_pipeline.py +++ b/q2_picrust2/_full_pipeline.py @@ -50,17 +50,18 @@ def full_pipeline(table: biom.Table, no_pathways=False, regroup_map=default_regroup_map, no_regroup=False, - metagenome_contrib=False, stratified=False, max_nsti=max_nsti, min_reads=1, min_samples=1, hsp_method=hsp_method, skip_nsti=False, - no_gap_fill=False, skip_minpath=False, + no_gap_fill=False, coverage=False, per_sequence_contrib=False, + wide_table=False, + skip_norm=False, remove_intermediate=False, verbose=True) diff --git a/q2_picrust2/citations.bib b/q2_picrust2/citations.bib index 01ac339..d57b498 100644 --- a/q2_picrust2/citations.bib +++ b/q2_picrust2/citations.bib @@ -1,12 +1,8 @@ -@article{Langille2013NatureBioTech, - title={Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences}, - author={Langille and Zaneveld et al.}, - journal={Nature Biotechnology}, - volume={31}, - number={9}, - pages={815-823}, - year={2013}, - publisher={Nature Publishing Group}, - doi={10.1038/nbt.2676} +@article{Douglas2019bioRxiv, + title={PICRUSt2: An improved and extensible approach for metagenome inference}, + author={Douglas et al.}, + journal={bioRxiv}, + year={2019}, + doi={10.1101/672295} } diff --git a/q2_picrust2/plugin_setup.py b/q2_picrust2/plugin_setup.py index 6e0a4f2..76d1c2a 100644 --- a/q2_picrust2/plugin_setup.py +++ b/q2_picrust2/plugin_setup.py @@ -13,13 +13,14 @@ plugin = Plugin( name='picrust2', - version="2019.4", + version="2019.7", website='https://github.com/gavinmdouglas/q2-picrust2', package='q2_picrust2', description=('This QIIME 2 plugin wraps the default 16S PICRUSt2 pipeline to run ' 'metagenome inference based on marker gene data. Currently ' 'only unstratified output is supported.'), short_description='Predicts gene families and pathways from 16S sequences.', + citations=[citations['Douglas2019bioRxiv']] ) plugin.methods.register_function( @@ -49,14 +50,14 @@ 'be output.')}, output_descriptions={'ko_metagenome': 'Predicted metagenome for KEGG orthologs', - 'ec_metagenome': 'Predicted metagenome for E.C. numbers', + 'ec_metagenome': 'Predicted metagenome for EC numbers', 'pathway_abundance': 'Predicted MetaCyc pathway abundances'}, name='Default 16S PICRUSt2 Pipeline', description=("QIIME2 Plugin for default 16S PICRUSt2 pipeline"), - citations=[citations['Langille2013NatureBioTech']] + citations=[citations['Douglas2019bioRxiv']] ) @@ -98,6 +99,6 @@ "used with the output of SEPP (q2-fragment-insertion) as a " + "starting point."), - citations=[citations['Langille2013NatureBioTech']] + citations=[citations['Douglas2019bioRxiv']] ) diff --git a/setup.py b/setup.py index ccde6c9..2483d58 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name="q2-picrust2", - version="2019.4", + version="2019.7", packages=find_packages(), package_data={'q2_picrust2': ['citations.bib']}, author="Gavin Douglas",