<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>