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comparison vcfgeno2haplo.xml @ 3:d6fd217a1f90 draft default tip

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author anton
date Mon, 15 Sep 2014 14:51:43 -0400
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2:a6cd013745fd 3:d6fd217a1f90
1 <tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.2"> 1 <tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.2">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="86723982aa">vcflib</requirement> 3 <requirement type="package" version="8a5602bf07">vcflib</requirement>
4 </requirements> 4 </requirements>
5 <description>Convert genotype-based phased alleles into haplotype alleles</description> 5 <description>Convert genotype-based phased alleles into haplotype alleles</description>
6 <command> 6 <command>
7 #set $reference_fasta_filename = "localref.fa" 7 #set $reference_fasta_filename = "localref.fa"
8 #if str( $reference_source.reference_source_selector ) == "history": 8 #if str( $reference_source.reference_source_selector ) == "history":
34 <when value="history"> <!-- FIX ME!!!! --> 34 <when value="history"> <!-- FIX ME!!!! -->
35 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> 35 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
36 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" /> 36 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset" />
37 </when> 37 </when>
38 </conditional> 38 </conditional>
39 <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)" /> 39 <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)" />
40 <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" /> 40 <param name="output_option" type="boolean" truevalue="-o" falsevalue="" label="What to report?" help="--only-variants option" />
41 <!-- <option value=" ">Output entire haplotype</option> 41 <!-- <option value=" ">Output entire haplotype</option>
42 <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option> 42 <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
43 </param> --> 43 </param> -->
44 </inputs> 44 </inputs>
62 62
63 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. 63 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.
64 64
65 The options are:: 65 The options are::
66 66
67 -r, --reference FILE FASTA reference file, required with -i and -u
68 -w, --window-size N Merge variants at most this many bp apart (default 30) 67 -w, --window-size N Merge variants at most this many bp apart (default 30)
69 -o, --only-variants Don't output the entire haplotype, just concatenate 68 -o, --only-variants Don't output the entire haplotype, just concatenate
70 REF/ALT strings (delimited by ":") 69 REF/ALT strings (delimited by ":")
71 70
72 ---- 71 ----