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comparison bcftools_view.xml @ 0:d4ab3121553d draft

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author iuc
date Thu, 14 Aug 2014 11:43:40 -0400
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1 <tool id="bcfview" name="bcftoolsView" version="0.1.19">
2 <description>Convert, filter, subset VCF/BCF files</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <expand macro="stdio" />
6 <macros>
7 <token name="@EXECUTABLE@">bcftools</token>
8 <import>bcftools_macros.xml</import>
9 </macros>
10 <command>
11 @EXECUTABLE@ view
12 $A
13 $varsitesonly
14 $snpcalling
15 ##$F
16 $G
17 $N
18 $e
19 $g
20
21 #if str( $output_format ) == "bcf":
22 -b
23 #end if
24
25 -D $seq_dict
26
27 -i $ratio
28 -t $rate
29
30 $input
31 &gt; $output
32
33 </command>
34 <inputs>
35 <param name="input" type="data" format="bcf,vcf" label="Choose a bcf file to view" />
36 <param name="output_format" type="select" label="Choose the output format" help="-b">
37 <option value="vcf" selected="true">VCF</option>
38 <option value="bcf">BCF</option>
39 </param>
40
41 <param name="seq_dict" type="data" format="tabular" optional="True" label="List of chromosome names for conversion" help="(-D)" />
42
43 <param name="ratio" type="float" label="Use alternate INDEL-to-SNP mutation rate" value="-1" help="defaults to 0.15 (-i)" />
44 <param name="rate" type="float" label="Mutation rate for variant calling" value="0.001" help="default to 0.001 (-t)" />
45
46 <param name="A" type="boolean" truevalue="-A" falsevalue="" checked="False"
47 label="Retain all possible alternate alleles at variant sites" help="-A" />
48 <param name="varsitesonly" type="boolean" truevalue="-v" falsevalue="" checked="false" label="Output Potential Variant Sites Only" help="-v"/>
49 <param name="snpcalling" type="boolean" truevalue="-c" falsevalue="" checked="false" label="SNP calling" help="Forces -e the max-likelihood inference parameter. (-c)"/>
50 <!--param name="F" type="boolean" truevalue="-F" falsevalue="" checked="False"
51 label="Indicate PL is generated by r921 or before (ordering is different)" help="-F" /-->
52 <param name="G" type="boolean" truevalue="-G" falsevalue="" checked="False"
53 label="Suppress all individual genotype information" help="-G" />
54 <param name="N" type="boolean" truevalue="-N" falsevalue="" checked="False"
55 label="Skip sites where the REF field is not A/C/G/T" help="-N" />
56 <param name="e" type="boolean" truevalue="-e" falsevalue="" checked="False"
57 label="Perform max-likelihood inference only"
58 help="Including estimating the site allele frequency, testing Hardy-Weinberg equilibrium and testing associations with LRT. (-e)" />
59 <param name="g" type="boolean" truevalue="-g" falsevalue="" checked="True"
60 label="Call per-sample genotypes at variant sites" help="-g" />
61 </inputs>
62
63 <outputs>
64 <data format="bcf" name="output">
65 <change_format>
66 <when input="output_format" value="vcf" format="vcf" />
67 </change_format>
68 </data>
69 </outputs>
70
71 <tests>
72 </tests>
73
74 <help>
75 <![CDATA[
76 **BCFTools View**
77
78 VCF/BCF conversion, view, subset and filter VCF/BCF files.
79
80
81 **Input format**
82
83 `BCF files <http://www.1000genomes.org/wiki/analysis/variant-call-format/bcf-binary-vcf-version-2/>`_
84
85 ------
86
87 **Outputs**
88
89 VCF or BCF files
90
91 ]]>
92 </help>
93 <expand macro="citations"/>
94 </tool>