--- a/kegg_maps_visualization.xml	Tue Dec 18 09:23:35 2018 -0500
+++ b/kegg_maps_visualization.xml	Tue Dec 18 09:38:13 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.18">
+<tool id="kegg_maps_visualization" name="KEGG maps visualization" version="2018.12.18.1">
     <description>of (differentially expressed) genes/proteins</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>
@@ -13,12 +13,12 @@
             --id_column="$input.ncol"
             --header="$input.header"  
         #end if
-        #if $pathways_section.species.pathways.pathways_id != "pathways_file"
-            --pathways_id="$pathways_section.species.pathways.pids" 
+        #if $species.pathways.pathways_id != "pathways_file"
+            --pathways_id="$species.pathways.pids" 
         #else 
-            --pathways_input="$pathways_section.species.pathways.file"
-            --header2="$pathways_section.species.pathways.header2"
-            --pathway_col="$pathways_section.species.pathways.ncol2"
+            --pathways_input="$species.pathways.file"
+            --header2="$species.pathways.header2"
+            --pathway_col="$species.pathways.ncol2"
         #end if
         --id_type="$id_type"  
         --native_kegg="$native"
@@ -31,8 +31,8 @@
             --fold_change_data="false"
         #end if
 
-        --species=${pathways_section.species.ref_file} 
-        --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $pathways_section.species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] } 
+        --species=${species.ref_file} 
+        --pathways_list=$__tool_directory__/${ filter( lambda x: str( x[0] ) == str( $species.ref_file ), $__app__.tool_data_tables['kegg_pathways_list_index'].get_fields() )[0][-1] } 
         --output="$text_output"
 
     ]]></command>