--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcfgeno2haplo.xml	Wed Jun 11 17:10:52 2014 -0400
@@ -0,0 +1,77 @@
+<tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.1">
+<requirements>
+    <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
+</requirements>
+  <description>Convert genotype-based phased alleles into haplotype alleles</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    
+  vcfgeno2haplo ${output_option} -w ${window_size} -r "${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="window_size" type="text" size="4" value="30" label="compare records up to this many bp away (window size)" help="--window-size option (default = 30)" />
+     <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
+<!--       <option value=" ">Output entire haplotype</option>
+       <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
+     </param> -->
+  </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="output_option" value="true" />
+      <param name="window_size" value="5000" />
+      <param name="input_vcf" value="vcflib-phix.vcf"/>
+      <param name="ref_file" value="vcflib-test-genome-phix.fa" />
+      <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
+    </test>
+    </tests>
+  <help>
+
+Convert genotype-based phased alleles within a window size specified by -w option into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input.
+
+The options are::
+
+    -r, --reference FILE    FASTA reference file, required with -i and -u
+    -w, --window-size N     Merge variants at most this many bp apart (default 30)
+    -o, --only-variants     Don't output the entire haplotype, just concatenate
+                            REF/ALT strings (delimited by ":")
+
+----
+
+Vcfgeno2haplo is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).                                                                                                                                 
+
+</help>
+</tool>