--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gecko/frags2align.xml	Thu Dec 13 07:59:25 2018 -0500
@@ -0,0 +1,13 @@
+<tool id="frags2align" name="Frags to align">
+  <description>Extract alignments from a binary Frags file</description>
+  <inputs>
+    <param name="fragsFile" type="data" format="frags" label="Frags file" help="Binary Frags file" />
+    <param name="fastaX" type="data" format="fasta" label="x Genome" help="Single genome file in fasta format"/>    
+    <param name="fastaY" type="data" value="fasta" label="y Genome" help="Single genome file in fasta format" />
+  </inputs>
+  <command>/home/galaxy-bitlab/galaxy/tools/gecko/bin/frags2align.sh $fragsFile $fastaX $fastaY $alignments </command>
+  <outputs>
+    <data name="alignments" format="txt" label="Frags to align for genomes  ${fastaX.name}_${fastaY.name}"/>
+  </outputs>
+</tool>
+