fix plugin setup

q2_katharoseq/plugin_setup.py

@@ -67,102 +67,9 @@
     description='KatharoSeq is high-throughput protocol combining laboratory '
                 'and bioinformatic methods that can differentiate a true '
                 'positive signal in samples with as few as 50 to 500 cells.',
-    citations=[citations['minich2018']]
-)
-
-
-plugin.methods.register_function(
-    function=estimating_biomass,
-    inputs={},
-    parameters={'total_reads': MetadataColumn[Numeric],
-                'control_cell_extraction': MetadataColumn[Numeric],
-                'positive_control_column': MetadataColumn[Categorical],
-                'positive_control_value': Str,
-                'extraction_mass_g': MetadataColumn[Numeric],
-                'min_total_reads': Int,
-                'pcr_template_vol': Int,
-                'dna_extract_vol': Int},
-    outputs=[('estimated_biomass', EstimatedBiomass)],
-    input_descriptions={},
-    parameter_descriptions={
-        'total_reads': 'The total sum of the reads or ASVs for each sample.',
-        'control_cell_extraction': (
-            'The estimated number of cells or genomes used as input to your '
-            'library prep. One may typically estimate this by determining the '
-            'total number of cells from a stock solution used to make '
-            'standard titrations. Each titration will have an estimated '
-            'number of microbial cells put into the extraction. The final '
-            'estimate will depend on the elution volume and the final volume '
-            'used into the library prep (e.g. 16S PCR).'),
-        'positive_control_column': (
-            'The column in the sample metadata that describes which samples '
-            'are and are not controls.'),
-        'positive_control_value': (
-            'The value in the control column that demarks which samples are '
-            'the positive controls.'),
-        'extraction_mass_g': (
-            'The column in the sample metadata that describes the sample '
-            '(e.g. stool, tissue, soil, etc) mass (in grams - typically '
-            'converted from mg)'),
-        'min_total_reads': 'The minimum threshold to apply.',
-        'pcr_template_vol': (
-            'The volume of DNA used as template in the '
-            'library prep (PCR reaction)'),
-        'dna_extract_vol': (
-            'The final elution volume used during DNA extraction')},
-    output_descriptions={
-        'estimated_biomass': (
-            'A dataframe containing the details on estimated biomass')
-        },
-    name='Estimate the biomass of samples using KatharoSeq controls.',
-    description='Estimate the biomass of samples using KatharoSeq controls.',
     citations=[]
 )
 
-
-plugin.visualizers.register_function(
-    function=read_count_threshold,
-    inputs={
-        'table': FeatureTable[Frequency]
-    },
-    parameters={
-        'control': Str % Choices(['zymobiomics', 'classic', 'atcc']),
-        'threshold': Int,
-        'positive_control_value': Str,
-        'positive_control_column': MetadataColumn[Categorical],
-        'cell_count_column': MetadataColumn[Numeric]
-    },
-    input_descriptions={
-        'table': (
-            'A FeatureTable collapsed to the genus level (level 6) that '
-            'contains the control samples.'
-        ),
-    },
-    parameter_descriptions={
-        'control': (
-            'The type of positive control used.'
-        ),
-        'threshold': (
-            'Threshold to use in calculating minimum frequency. '
-            'Must be int in [0,100].'
-        ),
-        'positive_control_value': (
-            'The value in the control column that demarks which samples are '
-            'the positive controls.'
-        ),
-        'positive_control_column': (
-            'The column in the sample metadata that describes which samples '
-            'are and are not controls.'
-        ),
-    },
-    name='Methods for the application of the KatharoSeq protocol',
-    description='KatharoSeq is high-throughput protocol combining laboratory '
-                'and bioinformatic methods that can differentiate a true '
-                'positive signal in samples with as few as 50 to 500 cells.',
-    citations=[citations['minich2018']]
-)
-
-
 plugin.methods.register_function(
     function=estimating_biomass,
     inputs={},