Mercurial > repos > bgruening > vt
comparison vt_normalize.xml @ 0:26babe3a66f1 draft default tip
planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0
author | bgruening |
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date | Sat, 04 Jun 2016 10:41:29 -0400 |
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-1:000000000000 | 0:26babe3a66f1 |
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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 <macros> | |
4 <import>vt_macros.xml</import> | |
5 <token name="@BINARY@">normalize</token> | |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <expand macro="stdio" /> | |
9 <expand macro="version_command" /> | |
10 <command> | |
11 <![CDATA[ | |
12 vt @BINARY@ | |
13 #if str($output_format) == 'bcf': | |
14 -o normalised.bcf | |
15 #else: | |
16 -o normalised.vcf | |
17 #end if | |
18 ##-q do not print options and summary [] | |
19 -w $window | |
20 | |
21 #if str( $intervals_file ) != 'None': | |
22 -I "${intervals_file}" | |
23 #end if | |
24 $n | |
25 ##-i intervals [] | |
26 | |
27 #if $reference_source.reference_source_selector != "history": | |
28 -r "${reference_source.reference_genome.fields.path}" | |
29 #else: | |
30 -r "${reference_source.reference_genome}" | |
31 #end if | |
32 | |
33 "${ infile }" | |
34 | |
35 && | |
36 ## For some reason, the file move will randomly produce empty files. | |
37 ## Wait two seconds to let the system close file handlers and clean up. | |
38 sleep 2 | |
39 && | |
40 | |
41 #if str($output_format) == 'bcf': | |
42 mv normalised.bcf "${ outfile }"; | |
43 #else: | |
44 mv normalised.vcf "${ outfile }"; | |
45 #end if | |
46 | |
47 ]]> | |
48 </command> | |
49 <inputs> | |
50 <param name="infile" type="data" format="vcf" label="VCF file to be normalised" /> | |
51 | |
52 <conditional name="reference_source"> | |
53 <param name="reference_source_selector" type="select" label="Choose the source for the reference list"> | |
54 <option value="cached" selected="True">Locally cached</option> | |
55 <option value="history">History</option> | |
56 </param> | |
57 <when value="cached"> | |
58 <param name="reference_genome" type="select" label="Using reference genome"> | |
59 <options from_data_table="fasta_indexes"> | |
60 <filter type="data_meta" ref="infile" key="dbkey" column="1" /> | |
61 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset" /> | |
62 </options> | |
63 </param> | |
64 </when> | |
65 <when value="history"> | |
66 <param name="reference_genome" type="data" format="fasta" label="Using reference file" /> | |
67 </when> | |
68 </conditional> | |
69 <param name="intervals_file" type="data" format="bed" optional="True" label="File containing list of intervals" /> | |
70 <param name="window" type="integer" value="10000" label="Window size for local sorting of variants" | |
71 help="(-w)"> | |
72 <validator type="in_range" min="0"/> | |
73 </param> | |
74 <param argument="-n" type="boolean" truevalue="-n" falsevalue="" | |
75 label="Do not fail when REF is inconsistent with reference sequence for non SNPs" | |
76 help=""/> | |
77 <param name="output_format" type="select" label="Choose the output format" help=""> | |
78 <option value="bcf">BCF</option> | |
79 <option value="vcf" selected="true">VCF</option> | |
80 </param> | |
81 </inputs> | |
82 <outputs> | |
83 <data name="outfile" format="vcf" label="${tool.name} on ${on_string}"> | |
84 <change_format> | |
85 <when input="output_format" value="bcf" format="bcf" /> | |
86 </change_format> | |
87 </data> | |
88 </outputs> | |
89 <tests> | |
90 <test> | |
91 <param name="infile" value="infile01.vcf" /> | |
92 <param name="reference_source_selector" value="history" /> | |
93 <param name="reference_genome" value="20.fa.bz2" /> | |
94 <param name="n" value="True" /> | |
95 <output name="outfile" file="normalize_result01.vcf" ftype="vcf" /> | |
96 </test> | |
97 </tests> | |
98 <help> | |
99 <![CDATA[ | |
100 **What it does** | |
101 | |
102 Normalize variants in a VCF file. Normalized variants may have their positions changed; in such cases, | |
103 the normalized variants are reordered and output in an ordered fashion. The local reordering takes place over a window of 10000 base pairs. | |
104 | |
105 @CITATION@ | |
106 ]]> | |
107 </help> | |
108 <expand macro="citations"/> | |
109 </tool> |