diff xmfa2gff3.xml @ 1:bca52822843e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/progressivemauve commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7

--- a/xmfa2gff3.xml	Wed Aug 17 14:46:55 2016 -0400
+++ b/xmfa2gff3.xml	Fri Sep 07 11:30:11 2018 -0400
@@ -4,19 +4,23 @@
   <macros>
     <import>macros.xml</import>
   </macros>
-  <expand macro="requirements"/>
+  <requirements>
+    <requirement type="package" version="2.7">python</requirement>
+    <requirement type="package" version="1.72">biopython</requirement>
+    <requirement type="package" version="0.6.4">bcbiogff</requirement>
+  </requirements>
   <expand macro="stdio"/>
   <version_command>python xmfa2gff3.py --version</version_command>
-  <command interpreter="python"><![CDATA[
-xmfa2gff3.py
+  <command><![CDATA[
+python '${__tool_directory__}/xmfa2gff3.py'
 $xmfa
 --window_size $window_size
 --relative_to $relative_to
 --sequences
 #for file in $sequences:
-    "${file}"
+  '${file}'
 #end for
-> $output
+> '$output'
 
 ]]></command>
   <inputs>
@@ -39,7 +43,7 @@
   </outputs>
   <tests>
       <test>
-          <param name="xmfa" value="1.xmfa"/>
+          <param name="xmfa" value="2.xmfa"/>
           <param name="sequences" value="karma.fa,phagey.fa" />
           <param name="window_size" value="10" />
           <param name="relative_to" value="1" />