Mercurial > repos > iuc > bcftools_concat

annotate bcftools_concat.xml @ 14:5ee777f9db23 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
author iuc
date Thu, 14 Oct 2021 09:59:21 +0000
parents 874cc12ae316
children fc47ffec447e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
1 <?xml version='1.0' encoding='utf-8'?>
12
874cc12ae316 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
iuc
parents: 9
diff changeset
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
3 <description>Concatenate or combine VCF/BCF files</description>
14
5ee777f9db23 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
iuc
parents: 12
diff changeset
4 <expand macro="bio_tools" />
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
5 <macros>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
6 <token name="@EXECUTABLE@">concat</token>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
7 <import>macros.xml</import>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
8 </macros>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
9 <expand macro="requirements" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
10 <expand macro="version_command" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
11 <command detect_errors="aggressive"><![CDATA[
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
12 @PREPARE_ENV@
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
13 @PREPARE_INPUT_FILES@
5
40174941cbda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents: 4
diff changeset
14 #set $section = $sec_restrict
40174941cbda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents: 4
diff changeset
15 @PREPARE_REGIONS_FILE@
40174941cbda planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents: 4
diff changeset
16
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
17 bcftools @EXECUTABLE@
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
18
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
19 ## Default section
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
20 #set $section = $sec_default
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
21
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
22 #if $section.mode.naive == "yes":
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
23 --naive
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
24 #else:
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
25 #if $section.mode.overlaps.allow_overlaps == 'yes':
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
26 --allow-overlaps
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
27 #if $section.mode.overlaps.rm_dups:
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
28 --rm-dups $section.mode.overlaps.rm_dups
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
29 #end if
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
30 #end if
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
31 ${section.mode.ligate}
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
32 #end if
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
33 ${section.compact_PS}
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
34 #if str($section.min_PQ):
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
35 --min-PQ ${section.min_PQ}
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
36 #end if
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
37
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
38 #set $section = $sec_restrict
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
39 @REGIONS@
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
40
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
41 @OUTPUT_TYPE@
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
42 @THREADS@
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
43
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
44 ## Primary Input/Outputs
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
45 @INPUT_FILES@
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
46 #if $sec_default.mode.naive == "yes" and $output_type == 'v':
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
47 > output.gz && bcftools index output.gz && bcftools view -O v -o '$output_file' output.gz
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
48 #else:
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
49 > '$output_file'
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
50 #end if
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
51 ]]></command>
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
52 <inputs>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
53 <expand macro="macro_inputs" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
54 <section name="sec_restrict" expanded="false" title="Restrict to">
9
398d2ccc4233 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 8
diff changeset
55 <expand macro="macro_restrict" />
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
56 </section>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
57 <section name="sec_default" expanded="true" title="Concat Options">
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
58 <conditional name="mode">
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
59 <param name="naive" type="select" label="naive concat">
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
60 <help><![CDATA[
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
61 --naive concatenates VCF or BCF files without recompression. This can be used used to combine results that were generated separately for each chromosome. This is very fast but requires that all files are of the same type (all VCF or all BCF) and have the same headers. This is because all tags and chromosome names in the BCF body rely on the implicit order of the contig and tag definitions in the header. Currently no sanity checks are in place. Dangerous, use with caution.
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
62 ]]></help>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
63 <option value="no">No </option>
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
64 <option value="yes">Yes </option>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
65 </param>
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
66 <when value="yes"/>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
67 <when value="no">
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
68 <conditional name="overlaps">
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
69 <param name="allow_overlaps" type="select" label="Allow Overlaps">
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
70 <help>
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
71 First coordinate of the next file can precede last record of the current file.
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
72 </help>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
73 <option value="yes">Yes </option>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
74 <option value="no">No </option>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
75 </param>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
76 <when value="yes">
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
77 <param name="rm_dups" type="select" label="Remove duplicate" optional="true">
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
78 <help><![CDATA[
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
79 Output duplicate records present in multiple files only once:
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
80 rm-dups <snps|indels|both|all|none>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
81 ]]></help>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
82 <option value="snps">snps - SNP records</option>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
83 <option value="indels">indels - indel records</option>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
84 <option value="both">both - both SNP and indel records</option>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
85 <option value="all">all - records</option>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
86 <option value="none">none - output multiple records instead</option>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
87 </param>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
88 </when>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
89 <when value="no"/>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
90 </conditional>
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
91 <param name="ligate" type="boolean" truevalue="--ligate" falsevalue="" label="Ligate"
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
92 help="Ligate phased VCFs by matching phase at overlapping haplotypes" />
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
93 </when>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
94 </conditional>
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
95 <param name="compact_PS" type="boolean" truevalue="--compact-PS" falsevalue="" label="Compact Ps"
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
96 help="Do not output PS tag at each site, only at the start of a new phase set block." />
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
97 <param name="min_PQ" type="integer" label="Min Pq" value="30" optional="true"
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
98 help="Break phase set if phasing quality is lower than &lt;int&gt;" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
99 </section>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
100 <expand macro="macro_select_output_type" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
101 </inputs>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
102 <outputs>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
103 <expand macro="macro_vcf_output"/>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
104 </outputs>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
105 <tests>
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
106 <test>
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
107 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
108 <param name="output_type" value="v" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
109 <output name="output_file">
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
110 <assert_contents>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
111 <has_text_matching expression="1\t100"/>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
112 <has_text_matching expression="3\t192"/>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
113 </assert_contents>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
114 </output>
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
115 </test>
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
116 <test>
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
117 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf" />
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
118 <param name="naive" value="yes" />
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
119 <param name="output_type" value="v" />
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
120 <output name="output_file">
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
121 <assert_contents>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
122 <has_text_matching expression="1\t100"/>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
123 <has_text_matching expression="3\t192"/>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
124 </assert_contents>
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
125 </output>
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
126 </test>
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
127 <test>
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
128 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
129 <param name="allow_overlaps" value="yes" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
130 <param name="output_type" value="v" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
131 <output name="output_file">
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
132 <assert_contents>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
133 <has_text_matching expression="2\t140\t.\tA\tG"/>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
134 <has_text_matching expression="2\t140\t.\tGT\tG"/>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
135 </assert_contents>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
136 </output>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
137 </test>
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
138 <test>
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
139 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
140 <param name="allow_overlaps" value="yes" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
141 <param name="rm_dups" value="none" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
142 <param name="output_type" value="v" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
143 <output name="output_file">
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
144 <assert_contents>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
145 <has_text_matching expression="2\t160\t.\tTAAAA"/>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
146 </assert_contents>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
147 </output>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
148 </test>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
149 </tests>
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
150 <help><![CDATA[
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
151 =====================================
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
152 bcftools @EXECUTABLE@ plugin
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
153 =====================================
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
154
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
155 Concatenate or combine VCF/BCF files. All source files must have the same sample columns appearing in the same order. The program can be used, for example, to concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel VCF into one. The input files must be sorted by chr and position. The files must be given in the correct order to produce sorted VCF on output unless the -a, --allow-overlaps option is specified.
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
156
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
157
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
158 Naive concatenation is useful when using a galaxy workflow that splits a BAM file by chromosome, processes each in parallel, then bcftools concat merges the results into a single VCF file:
6
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
159
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
160 BAM -> bamtools split => bcftools mpileup => bcftools call => bcftools concat -> VCF
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
161
2d95ed0b720a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e2075caee2ecdc6aed15a356e5328c5ca09cfb13
iuc
parents: 5
diff changeset
162
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
163 @REGIONS_HELP@
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
164
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
165 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
166
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
167 @BCFTOOLS_WIKI@
8
62ca6da715bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 6
diff changeset
168 ]]></help>
0
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
169 <expand macro="citations" />
dda05d07d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
170 </tool>