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comparison vcfgeno2haplo.xml @ 0:e19406b6e652

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Imported from capsule None
author anton
date Wed, 11 Jun 2014 17:10:52 -0400
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1 <tool id="vcfgeno2haplo" name="VCFgenotype-to-haplotype:" version="0.0.1">
2 <requirements>
3 <requirement type="package" version="586c5ae5d57a38dae6b32ea831fb1f7cfa14c9bd">vcflib</requirement>
4 </requirements>
5 <description>Convert genotype-based phased alleles into haplotype alleles</description>
6 <command>
7 #set $reference_fasta_filename = "localref.fa"
8 #if str( $reference_source.reference_source_selector ) == "history":
9 ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
10 #else:
11 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
12 #end if
13 vcfgeno2haplo ${output_option} -w ${window_size} -r "${reference_fasta_filename}" "${input_vcf}" > "${out_file1}"</command>
14 <inputs>
15 <conditional name="reference_source">
16 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
17 <option value="cached">Locally cached</option>
18 <option value="history">History</option>
19 </param>
20 <when value="cached">
21 <param name="ref_file" type="select" label="Select reference genome">
22 <options from_data_table="fasta_indexes">
23 <!--<filter type="data_meta" key="dbkey" ref="input_bam" column="value"/>-->
24 </options>
25 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
26 </param>
27 <param name="input_vcf" type="data" format="vcf" label="Select VCF dataset">
28 <!-- Validators are commented to allow users apply too to any build. May need to be revised in the future
29 <validator type="unspecified_build" />
30 <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." />
31 -->
32 </param>
33 </when>
34 <when value="history"> <!-- FIX ME!!!! -->
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" />
37 </when>
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)" />
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>
42 <option value="-o">Don't output the entire haplotype, just concatenate REF/ALT strings (delimited by &quot;:&quot;)</option>
43 </param> -->
44 </inputs>
45 <outputs>
46 <data format="vcf" name="out_file1" />
47 </outputs>
48 <stdio>
49 <exit_code range="1:" level="fatal" />
50 </stdio>
51 <tests>
52 <test>
53 <param name="reference_source_selector" value="history" />
54 <param name="output_option" value="true" />
55 <param name="window_size" value="5000" />
56 <param name="input_vcf" value="vcflib-phix.vcf"/>
57 <param name="ref_file" value="vcflib-test-genome-phix.fa" />
58 <output name="out_file1" file="vcfgeno2haplo-test1.vcf"/>
59 </test>
60 </tests>
61 <help>
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.
64
65 The options are::
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)
69 -o, --only-variants Don't output the entire haplotype, just concatenate
70 REF/ALT strings (delimited by ":")
71
72 ----
73
74 Vcfgeno2haplo is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib).
75
76 </help>
77 </tool>