--- a/cfsan_lexmapr2.xml	Wed Aug 31 14:32:14 2022 -0400
+++ b/cfsan_lexmapr2.xml	Tue Sep 13 11:32:24 2022 -0400
@@ -28,7 +28,7 @@
     #end for
     ]]></command>
     <environment_variables>
-        <environment_variable name="NLTK_DATA">$__tool_directory__/nltk_data</environment_variable>
+        <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
     </environment_variables>
     <inputs>
         <param name="input" type="data" format="csv" label="Input CSV"
@@ -71,6 +71,30 @@
         - group mapped results by parent ontologies
         - visualize mapping results
 
+----
+
+.. class:: infomark
+
+**Customization**
+
+By default, the FOODON and NCBITaxon ontologies are used. Users can define a comma-delimited list of ontology short names (https://www.ebi.ac.uk/ols/ontologies) flagged with '-e'. Bins are used to categorize matched ontologies by their parent ontologies. Users can override the default bins by flagging a JSON file with the '-u' option.
+
+Example JSON format to use a bin titled 'ncbi_taxon':
+
+    ::
+
+        {
+            "ncbi_taxon":{
+                "Actinopterygii":"NCBITaxon_7898",
+                "Ecdysozoa":"NCBITaxon_1206794",
+                "Echinodermata":"NCBITaxon_7586",
+                "Fungi":"NCBITaxon_4751",
+                "Mammalia":"NCBITaxon_40674",
+                "Sauropsida":"NCBITaxon_8457",
+                "Spiralia":"NCBITaxon_2697495",
+                "Viridiplantae":"NCBITaxon_33090"
+            }
+        }
 
 ----
 
@@ -82,11 +106,9 @@
 
     ::
 
-        - An tab-seperated file with matched annotations.
+        - An tab-seperated file with possible matched annotations.
         - A list of Lexmapr2 figures in PNG format.
 
-        
-
   ]]></help>
     <citations>
         <citation type="bibtex">