Merge pull request #10 from gavinmdouglas/2019.7

2019.7

Author: gavinmdouglas

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)
 

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}
 }
 

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']]
 )
 

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",