--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfleftalign.xml	Wed Jun 11 17:12:06 2014 -0400
@@ -0,0 +1,59 @@
+<tool id="vcfleftalign" name="VCFleftAlign:" version="0.0.1">
+<requirements>
+    <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
+    <!-- <requirement type="package" version="0.1.18">samtools</requirement> -->
+</requirements>
+  <description>Left-align indels and complex variants in VCF dataset</description>
+  <command>
+    #set $reference_fasta_filename = "localref.fa"
+    #if str( $reference_source.reference_source_selector ) == "history":
+       ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+    #else:
+       #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+    #end if    
+   vcfleftalign -r "${reference_fasta_filename}" -w "${window_size}" "${input_vcf}" > "${out_file1}"</command>
+  <inputs>
+<param name="input_vcf" type="data" format="vcf" label="VCF dataset to left-align" />
+    <conditional name="reference_source">
+       <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+         <option value="cached">Locally cached</option>
+         <option value="history">History</option>
+       </param>
+       <when value="cached">
+         <param name="ref_file" type="select" label="Select reference genome">
+           <options from_data_table="fasta_indexes">
+           </options>
+	   <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+         </param>
+       </when>
+       <when value="history"> <!-- FIX ME!!!! -->
+         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+       </when>
+     </conditional>
+     <param name="window_size" type="integer" value="150" label="Use a window of this many bp when left-aligning" help="default = 150 bp" />
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+ <stdio>
+    <exit_code range="1:" level="fatal" />
+ </stdio>
+  <tests>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="input_vcf" value="vcflib-phix.vcf"/>
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
+      <param name="window_size" value="150" />
+      <output name="out_file1" file="vcfleftalign-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Left-aligns variants in VCF dataset.  Window size is determined dynamically according to the entropy of the regions flanking the indel.  These must have entropy > 1 bit/bp, or be shorter than ~5kb.
+
+----
+
+Vcfleftalign is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
+
+</help>
+</tool>