comparison vcfgeno2haplo.xml @ 3:d6fd217a1f90 draft default tip

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<tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.2">
<requirements>
    <requirement type="package" version="86723982aa">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":

       <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>

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 ":")

----

3:d6fd217a1f90

<tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.2">
<requirements>
    <requirement type="package" version="8a5602bf07">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":

       <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" 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>

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::

    -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 ":")

----