diff substitutions.xml @ 1:aca54f2b2151 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/substitutions commit f929353ffb0623f2218d7dec459c7da62f3b0d24"

--- a/substitutions.xml	Tue Apr 01 10:50:41 2014 -0400
+++ b/substitutions.xml	Mon Jul 06 20:34:54 2020 -0400
@@ -1,24 +1,26 @@
-<tool id="substitutions1" name="Fetch substitutions " version="1.0.0">
-  <description> from pairwise alignments</description>
-  <command interpreter="python">
-  	substitutions.py 
-  	$input 
-  	$out_file1
-  </command>
-  <inputs>
-    <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
-  </inputs>
-  <outputs>
-    <data format="tabular" name="out_file1" metadata_source="input"/>
-  </outputs>
-
-  <tests>
-    <test>
-      <param name="input" value="Interval2Maf_pairwise_out.maf"/>
-      <output name="out_file1" file="subs.out"/>
-    </test>
-  </tests>
- <help> 
+<tool id="substitutions1" name="Fetch substitutions " version="1.0.1">
+    <description> from pairwise alignments</description>
+    <requirements>
+        <requirement type="package" version="0.8.8">bx-python</requirement>
+    </requirements>
+    <command>
+        python '$__tool_directory__/substitutions.py'
+            '$input'
+            '$out_file1'
+    </command>
+    <inputs>
+        <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="out_file1" metadata_source="input"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="Interval2Maf_pairwise_out.maf"/>
+            <output name="out_file1" file="subs.out"/>
+        </test>
+    </tests>
+    <help>
 
 .. class:: infomark
 
@@ -34,5 +36,5 @@
 
 Any block/s not containing exactly two sequences, will be omitted. 
 
-  </help>  
-</tool>
\ No newline at end of file
+    </help>
+</tool>