Mercurial > repos > bgruening > vt

annotate vt_normalize.xml @ 0:26babe3a66f1 draft default tip

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