# HG changeset patch
# User kkonganti
# Date 1663260773 14400
# Node ID 6fc05c435932170b56eb43012cbb475a6b7f8195
# Parent  91438d32ed5873958fd74f3330598e2034e5334a
"planemo upload"

diff -r 91438d32ed58 -r 6fc05c435932 cfsan_lexmapr2.xml
--- a/cfsan_lexmapr2.xml	Wed Sep 14 10:39:29 2022 -0400
+++ b/cfsan_lexmapr2.xml	Thu Sep 15 12:52:53 2022 -0400
@@ -21,11 +21,10 @@
     $bins
     $full
     $graph
-    #for $in_json in $input_json
-        #if $in_json
-            -u "$in_json"
-        #end if
-    #end for
+    #if $input_json.json_is_set
+        -u "$input_json.upload"
+    #end if
+    $input
     ]]></command>
     <environment_variables>
         <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>
@@ -33,8 +32,14 @@
     <inputs>
         <param name="input" type="data" format="csv" label="Input CSV"
             help="First row should be a header and first column should be sample names" />
-        <param name="input_json" type="data" format="json" optional="true"
-            label="User defined bins in JSON format" />
+        <conditional name="input_json">
+            <param name="json_is_set" type="boolean" label="Use User defined bins in JSON format?" />
+            <when value="true">
+                <param name="upload" type="data" format="json" label="User defined bins" />
+            </when>
+            <when value="false">
+            </when>
+        </conditional>
         <param name="embl_ont" type="text" optional="true" 
             label="User defined comma-separated EMBL Ontology short names" />
         <param name="bins" truevalue="-b" type="boolean" checked="true"