# HG changeset patch
# User kkonganti
# Date 1663261591 14400
# Node ID b959a72ca0b5d04a4cc40cea1aab6d9987e15409
# Parent  c56b568f3dde5d2a358bedaf91fb0eb32c99e7df
"planemo upload"

diff -r c56b568f3dde -r b959a72ca0b5 cfsan_lexmapr2.xml
--- a/cfsan_lexmapr2.xml	Thu Sep 15 13:03:18 2022 -0400
+++ b/cfsan_lexmapr2.xml	Thu Sep 15 13:06:31 2022 -0400
@@ -13,6 +13,8 @@
     </requirements>
     <version_command>python $__tool_directory__/lexmapr2.py --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
+    mkdir -p lexmapr2-input || exit 1;
+    ln -sf '$input' './lexmapr2-input/$input.name';
     python $__tool_directory__/lexmapr2.py
     #if ($embl_ont != ""):
         -e $embl_ont
@@ -32,7 +34,7 @@
     #if $input_json.json_is_set:
         -u "$input_json.upload"
     #end if
-    $input
+    ./lexmapr2-input/$input.name
     ]]></command>
     <environment_variables>
         <environment_variable name="NLTK_DATA">/tool/tool-data/cfsan_lexmapr2/0/nltk_data</environment_variable>