Merge pull request #6 from dpear/add-tutorial

update readme

README.md

@@ -14,16 +14,29 @@ pip install -e .
 
 ## Use
 
+Computation assumes that the user has classified their 16S features against SILVA, and that the `FeatureTable[Frequency]` has been collapsed to the genus level. Please see the [`q2-feature-classifier`](https://docs.qiime2.org/2021.11/plugins/available/feature-classifier/classify-sklearn) for detail on how to perform taxonomy
+classification, and the [`q2-taxa`](https://docs.qiime2.org/2021.11/plugins/available/taxa/collapse) plugin for information on collapsing to a taxonomic level. If you need more information on how to process your data, please refer to one of the relevant tutorials that can be found [here](https://docs.qiime2.org/2022.2/tutorials/).
+
+
+## Obtaining a read count threshold
+
 Computation of a minimum read count threshold can be performed with the
-`read_count_threshold` plugin action. Computation assumes that the user has
-classified their 16S features against SILVA, and that the
-`FeatureTable[Frequency]` has been collapsed to the genus level. Please see the
-[`q2-feature-classifier`](https://docs.qiime2.org/2021.11/plugins/available/feature-classifier/classify-sklearn) for detail on how to perform taxonomy
-classification, and the [`q2-taxa`](https://docs.qiime2.org/2021.11/plugins/available/taxa/collapse) plugin for information on collapsing to a taxonomic level.
+`read_count_threshold` plugin action. Test data can be found under the `testdata` folder.
 
 ```
 qiime katharoseq read_count_threshold \
-    --i-table a_genus_level_table.qza \
+    --i-table example/example_table_genus.qza  \ # a genus level table
+    --p-threshold 80 \
+    --p-control classic \
+    --p-positive-control-value katharoseq_control \ # name of controls in metadata
+    --m-positive-control-column-file example/simple_katharoseq_metadata.tsv \ # your metadata
+    --m-positive-control-column-column control_or_sample \ # sample type variable in metadata
+    --m-cell-count-column-file example/simple_katharoseq_metadata.tsv \
+    --m-cell-count-column-column max_cell_count \ # cell count variable in metadata
+    --o-visualization result.qzv
+```
+qiime katharoseq read_count_threshold \
+    --i-table example.qza \ # a_genus_level_table
     --p-threshold 80 \
     --p-control classic \
     --p-positive-control-value name_of_controls_in_metadata \
@@ -32,4 +45,4 @@ qiime katharoseq read_count_threshold \
     --m-cell-count-column-file your_metadata.tsv \
     --m-cell-count-column-column cell_count_variable_in_metadata \
     --o-visualization result.qzv
-```
+```

setup.py

@@ -26,6 +26,7 @@
     },
     package_data={
         "q2_katharoseq": ['citations.bib'],
+        "example": ['*']
     },
     zip_safe=False,
     install_requires=['scipy',