--- a/find_subsequences.xml	Tue Apr 05 15:26:05 2016 -0400
+++ b/find_subsequences.xml	Wed Jul 12 11:51:17 2017 -0400
@@ -1,15 +1,14 @@
-<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.2">
+<tool id="bg_find_subsequences" name="Nucleotide subsequence search" version="0.3">
     <description>providing regions in BED format</description>
     <requirements>
-        <!-- Contains also the Conda dependency, see https://anaconda.org/anaconda/biopython -->
-        <requirement type="package" version="1.65">biopython</requirement>
+        <requirement type="package" version="1.70">biopython</requirement>
     </requirements>
-    <command interpreter="python">
+    <command>
     <![CDATA[
-        find_subsequences.py
-            --input "${input}"
-            --output "${output}"
-            --pattern "$pattern_conditional.pattern"
+        python '$__tool_directory__/find_subsequences.py'
+            --input '${input}'
+            --output '${output}'
+            --pattern '$pattern_conditional.pattern'
             #if $input.ext == 'fasta':
                 --format 'fasta'
             #else: