--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfcheck.xml	Wed Jun 11 17:11:46 2014 -0400
@@ -0,0 +1,73 @@
+<tool id="vcfcheck" name="VCFcheck:" version="0.0.1">
+<requirements>
+    <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
+</requirements>
+  <description>Verify that the reference allele matches the reference genome</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    
+  vcfcheck $failure_selector -f "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
+  <inputs>
+    <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">
+             <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
+           </options>
+	   <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+         </param>
+	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
+	   <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
+		<validator type="unspecified_build" />
+		<validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+	   -->
+	 </param>
+       </when>
+       <when value="history"> <!-- FIX ME!!!! -->
+         <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+	 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
+       </when>
+     </conditional>
+     <param name="failure_selector" type="select" display="radio" label="Exclude or include failed sites">
+       <option value="-x">Exculde failures (-x option)</option>
+       <option value="-k">Keep failures (-k option)</option>
+     </param>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="out_file1" />
+  </outputs>
+  <stdio>
+    <regex match="index file" source="stderr" level="warning"/>
+  </stdio>
+  <tests>
+    <test>
+      <param name="reference_source_selector" value="history" />
+      <param name="failure_selection" value="-x" />
+      <param name="input_vcf" value="vcflib-phix.vcf"/>
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
+      <output name="out_file1" file="vcfcheck-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Verifies that the VCF REF field matches the reference as described.  
+
+The options are::
+
+    -x, --exclude-failures If a record fails, don't print it.  Otherwise do.
+    -k, --keep-failures    Print if the record fails, otherwise not.
+
+----
+
+Vcfcheck is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
+
+</help>
+</tool>