--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfprimers.xml	Thu Mar 19 14:43:10 2015 -0400
@@ -0,0 +1,67 @@
+<tool id="vcfprimers" name="VCFprimers:" version="0.0.3">
+  <description>Extract flanking sequences for each VCF record</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="stdio"></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( $reference_source.ref_file.fields.path )
+    #end if    
+   vcfprimers -f "${reference_fasta_filename}" -l "${primer_length}" "${input_vcf}" > "${out_file1}"</command>
+  <inputs>
+<param name="input_vcf" type="data" format="vcf" label="VCF dataset to extract flanks" />
+    <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="primer_length" type="integer" value="20" label="The length of the primer sequences on each side of the variant" help="default = 20 bp" />
+  </inputs>
+  <outputs>
+    <data format="fasta" name="out_file1" />
+  </outputs>
+  <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="primer_length" value="5" />
+      <output name="out_file1" file="vcfprimers-test1.fasta"/>
+    </test>
+    </tests>
+  <help>
+
+For each VCF record, extract the flanking sequences, and write them as FASTA
+records suitable for alignment.  This tool is intended for use in designing validation
+experiments.  Primers extracted which would flank all of the alleles at multi-allelic
+sites.  The name of the FASTA "reads" indicates the VCF record which they apply to.
+The form is >CHROM_POS_LEFT for the 3' primer and >CHROM_POS_RIGHT for the 5' primer,
+for example::
+
+ >20_233255_LEFT
+ CCATTGTATATATAGACCATAATTTCTTTATCCAATCATCTGTTGATGGA
+ >20_233255_RIGHT
+ ACTCAGTTGATTCCATACCTTTGCCATCATGAATCATGTTGTAATAAACA
+
+----
+
+Vcfprimers @IS_PART_OF_VCFLIB@
+</help>
+  <expand macro="citations" />
+</tool>