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comparison vt_normalize.xml @ 0:e4d445a95419 draft

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author iuc
date Mon, 11 Aug 2014 14:10:22 -0400
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1 <tool id="vt_@BINARY@" name="VT @BINARY@" version="@VERSION@.0">
2 <description>normalizes variants in a VCF file</description>
3 <expand macro="requirements" />
4 <expand macro="version_command" />
5 <macros>
6 <import>vt_macros.xml</import>
7 <token name="@BINARY@">normalize</token>
8 </macros>
9 <command>
10 <![CDATA[
11 vt @BINARY@
12 -o "${ outfile }"
13 ##-q do not print options and summary []
14 -w window size for local sorting of variants [10000]
15 -I $intervals_file
16 ##-i intervals []
17 -r $reference_genome
18 "${ infile }"
19 ]]>
20 </command>
21 <expand macro="stdio" />
22 <inputs>
23 <param name="infile" type="data" format="sqlite" label="GEMINI database" />
24
25 <param name="reference_genome" type="select" label="Using reference genome">
26 <options from_data_table="fasta_indexes">
27 <filter type="data_meta" ref="infile" key="dbkey" column="1" />
28 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" />
29 </options>
30 </param>
31
32 <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" />
33 <param name="window" type="integer" value="10000" size="10" label="Window size for local sorting of variants"
34 help="(-w)">
35 <validator type="in_range" min="0"/>
36 </param>
37
38 </inputs>
39 <outputs>
40 <data name="outfile" format="vcf" label="${tool.name} on ${on_string}" />
41 </outputs>
42 <tests>
43 <test>
44 </test>
45 </tests>
46 <help>
47 **What it does**
48
49 Normalize variants in a VCF file. Normalized variants may have their positions changed; in such cases,
50 the normalized variants are reordered and output in an ordered fashion. The local reordering takes place over a window of 10000 base pairs.
51
52 @CITATION@
53 </help>
54 <!--expand macro="citations"/-->
55 </tool>