From 8eac1b62d137ef60219f782cd84daa2f70210ebe Mon Sep 17 00:00:00 2001
From: AmandaBirmingham <lists@imladris.com>
Date: Wed, 2 Oct 2024 13:26:18 -0700
Subject: [PATCH] extend docs for optional parameter

---
 README.md                                 | 19 +++++++++++++++++--
 q2_surpi/tests/data/surpi_sample_info.csv |  2 +-
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index c90ffff..7ffc5ef 100644
--- a/README.md
+++ b/README.md
@@ -37,14 +37,16 @@ qiime tools import \
     --type SurpiCountTable
 
 qiime tools import \
-    --input-path surpi_sample_sheet.txt \
+    --input-path surpi_sample_info.csv \
     --output-path surpi_sample_info.qza \
     --type SurpiSampleSheet
 ```
 
 With these artifacts, it is simple to extract a `FeatureTable[Frequency]` 
 QIIME object containing the counts generated by SURPI, as well as a 
-`FeatureData[Taxonomy]` QIIME object containing the associated taxonomies:
+`FeatureData[Taxonomy]` QIIME object containing the associated taxonomies.  
+Assuming that the SURPI sample sheet is linked to the counttable files by 
+barcode IDs, this can be accomplished by running:
 
 ```
 qiime surpi extract \
@@ -54,5 +56,18 @@ qiime surpi extract \
      --o-taxonomy surpi_taxonomy.qza
 ```
 
+Alternatively, if the sample sheet and counttable files are linked by the Sample_ID 
+values, the command can be altered to set the optional `--p-ids-are-barcodes` 
+parameter to `False`
+
+```
+qiime surpi extract \
+     --i-surpi-output surpi_output_by_sample_id.qza \
+     --i-surpi-sample-info surpi_sample_info.qza \
+     --p-ids-are-barcodes False \
+     --o-table surpi_counts.qza \
+     --o-taxonomy surpi_taxonomy.qza
+```
+
 These objects are suitable for use in downstream QIIME functions such as 
 `qiime diversity core-metrics-phylogenetic` or `qiime taxa barplot`.
\ No newline at end of file
diff --git a/q2_surpi/tests/data/surpi_sample_info.csv b/q2_surpi/tests/data/surpi_sample_info.csv
index 882e24c..21743d0 100644
--- a/q2_surpi/tests/data/surpi_sample_info.csv
+++ b/q2_surpi/tests/data/surpi_sample_info.csv
@@ -4,7 +4,7 @@ IEMFileVersion,4,,,,,,,,
 ,,,,,,,,,
 Investigator Name,VS,,,,,,,,
 ,,,,,,,,,
-Experiment Name,WW_NS_230126_qiime,,,,,,,,
+Experiment Name,qiime_test,,,,,,,,
 ,,,,,,,,,
 Date,1/26/23,,,,,,,,
 ,,,,,,,,,