--- a/vcfcheck.xml	Wed Nov 11 12:58:33 2015 -0500
+++ b/vcfcheck.xml	Thu Sep 15 16:04:23 2016 -0400
@@ -1,74 +1,74 @@
-<tool id="vcfcheck" name="VCFcheck:" version="0.0.3">
-  <description>Verify that the reference allele matches the reference genome</description>
-  <macros>
-    <import>macros.xml</import>
-  </macros>
-  <expand macro="requirements"></expand>
-  <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_PART_OF_VCFLIB@
-</help>
-  <expand macro="citations" />
-</tool>
+<tool id="vcfcheck" name="VCFcheck:" version="@WRAPPER_VERSION@.0">
+    <description>Verify that the reference allele matches the reference genome</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"></expand>
+    <stdio>
+        <regex match="index file" source="stderr" level="warning"/>
+    </stdio>
+    <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>
+    <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_PART_OF_VCFLIB@
+    </help>
+    <expand macro="citations" />
+</tool>