Mercurial > repos > iuc > bcftools_concat

annotate bcftools_concat.xml @ 26:11c2dc7762b8 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/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
author iuc
date Tue, 02 Dec 2025 07:50:00 +0000
parents c16fe9d71fe1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
19
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
2 <description>Concatenate or combine VCF/BCF files</description>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
3 <macros>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
4 <token name="@EXECUTABLE@">concat</token>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
5 <import>macros.xml</import>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
6 </macros>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
7 <expand macro="bio_tools"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
8 <expand macro="requirements"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
9 <expand macro="version_command"/>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
10 <command detect_errors="aggressive"><![CDATA[
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
11 @PREPARE_INPUT_FILES@
5
d235ff3501fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents: 4
diff changeset
12 #set $section = $sec_restrict
d235ff3501fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents: 4
diff changeset
13 @PREPARE_REGIONS_FILE@
d235ff3501fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents: 4
diff changeset
14
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
15 bcftools @EXECUTABLE@
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
16
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
17 ## Default section
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
18 #set $section = $sec_default
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
19
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
20 #if $section.mode.naive == "yes":
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
21 --naive
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
22 #else:
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
23 #if $section.mode.overlaps.allow_overlaps == 'yes':
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
24 --allow-overlaps
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
25 #if $section.mode.overlaps.rm_dups:
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
26 --rm-dups $section.mode.overlaps.rm_dups
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
27 #end if
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
28 #end if
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
29 ${section.mode.ligate}
19
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
30 #if $section.mode.ligate_mode
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
31 $section.mode.ligate_mode
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
32 #end if
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
33 #end if
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
34 ${section.compact_PS}
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
35 #if str($section.min_PQ):
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
36 --min-PQ ${section.min_PQ}
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
37 #end if
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
38
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
39 #set $section = $sec_restrict
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
40 @REGIONS@
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
41
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
42 @OUTPUT_TYPE@
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
43 @THREADS@
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
44
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
45 ## Primary Input/Outputs
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
46 @INPUT_FILES@
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
47 #if $sec_default.mode.naive == "yes" and $output_type == 'v':
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
48 > output.gz && bcftools index output.gz && bcftools view -O v -o '$output_file' output.gz
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
49 #else:
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
50 > '$output_file'
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
51 #end if
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
52 ]]></command>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
53 <inputs>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
54 <expand macro="macro_inputs"/>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
55 <section name="sec_restrict" expanded="false" title="Restrict to">
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
56 <expand macro="macro_region_restrict"/>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
57 </section>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
58 <section name="sec_default" expanded="true" title="Concat Options">
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
59 <conditional name="mode">
19
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
60 <param argument="--naive" type="select" label="Naive concat">
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
61 <help><![CDATA[
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
62 --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.
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
63 ]]></help>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
64 <option value="no">No </option>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
65 <option value="yes">Yes </option>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
66 </param>
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
67 <when value="yes"/>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
68 <when value="no">
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
69 <conditional name="overlaps">
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
70 <param name="allow_overlaps" type="select" label="Allow Overlaps">
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
71 <help>
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
72 First coordinate of the next file can precede last record of the current file.
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
73 </help>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
74 <option value="yes">Yes </option>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
75 <option value="no">No </option>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
76 </param>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
77 <when value="yes">
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
78 <param name="rm_dups" type="select" label="Remove duplicate" optional="true">
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
79 <help><![CDATA[
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
80 Output duplicate records present in multiple files only once:
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
81 rm-dups <snps|indels|both|all|none>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
82 ]]></help>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
83 <option value="snps">snps - SNP records</option>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
84 <option value="indels">indels - indel records</option>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
85 <option value="both">both - both SNP and indel records</option>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
86 <option value="all">all - records</option>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
87 <option value="none">none - output multiple records instead</option>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
88 </param>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
89 </when>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
90 <when value="no"/>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
91 </conditional>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
92 <param name="ligate" type="boolean" truevalue="--ligate" falsevalue="" label="Ligate" help="Ligate phased VCFs by matching phase at overlapping haplotypes"/>
19
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
93 <param name="ligate_mode" type="select" optional="true" label="Ligate mode" help="It allows finer control of --ligate behavior">
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
94 <option value="--ligate-warn">Ligate warn: Drop sites that are present in one chunk but absent in the other (--ligate-warn)</option>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
95 <option value="--ligate-force">Ligate force: Kepp sites that are present only in one chunk (--ligate-force)</option>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
96 </param>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
97 </when>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
98 </conditional>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
99 <param name="compact_PS" type="boolean" truevalue="--compact-PS" falsevalue="" label="Compact Ps" help="Do not output PS tag at each site, only at the start of a new phase set block."/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
100 <param name="min_PQ" type="integer" label="Min Pq" value="30" optional="true" help="Break phase set if phasing quality is lower than &lt;int&gt;"/>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
101 </section>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
102 <expand macro="macro_select_output_type"/>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
103 </inputs>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
104 <outputs>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
105 <expand macro="macro_vcf_output"/>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
106 </outputs>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
107 <tests>
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
108 <test>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
109 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
110 <param name="output_type" value="v"/>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
111 <output name="output_file">
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
112 <assert_contents>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
113 <has_text_matching expression="1\t100"/>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
114 <has_text_matching expression="3\t192"/>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
115 </assert_contents>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
116 </output>
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
117 </test>
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
118 <test>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
119 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
120 <section name="sec_default">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
121 <conditional name="mode">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
122 <param name="naive" value="no"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
123 </conditional>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
124 </section>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
125 <param name="output_type" value="v"/>
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
126 <output name="output_file">
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
127 <assert_contents>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
128 <has_text_matching expression="1\t100"/>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
129 <has_text_matching expression="3\t192"/>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
130 </assert_contents>
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
131 </output>
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
132 </test>
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
133 <test>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
134 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
135 <section name="sec_default">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
136 <conditional name="mode">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
137 <param name="naive" value="no"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
138 <conditional name="overlaps">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
139 <param name="allow_overlaps" value="yes"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
140 </conditional>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
141 </conditional>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
142 </section>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
143 <param name="output_type" value="v"/>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
144 <output name="output_file">
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
145 <assert_contents>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
146 <has_text_matching expression="2\t140\t.\tA\tG"/>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
147 <has_text_matching expression="2\t140\t.\tGT\tG"/>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
148 </assert_contents>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
149 </output>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
150 </test>
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
151 <test>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
152 <param name="input_files" ftype="vcf" value="concat.2.b.vcf,concat.2.a.vcf"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
153 <section name="sec_default">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
154 <conditional name="mode">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
155 <param name="naive" value="no"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
156 <conditional name="overlaps">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
157 <param name="allow_overlaps" value="yes"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
158 <param name="rm_dups" value="none"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
159 </conditional>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
160 </conditional>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
161 </section>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
162 <param name="output_type" value="v"/>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
163 <output name="output_file">
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
164 <assert_contents>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
165 <has_text_matching expression="2\t160\t.\tTAAAA"/>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
166 </assert_contents>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
167 </output>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
168 </test>
19
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
169 <!-- Test region overlap-->
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
170 <test>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
171 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
172 <param name="output_type" value="v"/>
19
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
173 <section name="sec_restrict">
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
174 <conditional name="regions">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
175 <param name="regions_src" value="regions" />
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
176 <repeat name="region_specs">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
177 <param name="chrom" value="1" />
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
178 </repeat>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
179 <repeat name="region_specs">
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
180 <param name="chrom" value="3" />
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
181 </repeat>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
182 </conditional>
19
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
183 </section>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
184 <output name="output_file">
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
185 <assert_contents>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
186 <has_text_matching expression="1\t100"/>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
187 <has_text_matching expression="3\t192"/>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
188 </assert_contents>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
189 </output>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
190 <assert_command>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
191 <has_text text="--regions-overlap"/>
19
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
192 </assert_command>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
193 </test>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
194 <!-- Test ligate options -->
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
195 <test>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
196 <param name="input_files" ftype="vcf" value="concat.1.b.vcf,concat.1.a.vcf"/>
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
197 <param name="output_type" value="v"/>
19
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
198 <section name="sec_default">
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
199 <conditional name="mode">
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
200 <conditional name="overlaps">
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
201 <param name="allow_overlaps" value="no"/>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
202 </conditional>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
203 <param name="ligate" value="true"/>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
204 <param name="ligate_mode" value="--ligate-warn"/>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
205 </conditional>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
206 </section>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
207 <output name="output_file">
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
208 <assert_contents>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
209 <has_text_matching expression="1\t100"/>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
210 <has_text_matching expression="3\t192"/>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
211 </assert_contents>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
212 </output>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
213 <assert_command>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
214 <has_text text="--ligate-warn"/>
19
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
215 </assert_command>
c16fe9d71fe1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 17
diff changeset
216 </test>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
217 </tests>
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
218 <help><![CDATA[
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
219 =====================================
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
220 bcftools @EXECUTABLE@ plugin
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
221 =====================================
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
222
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
223 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.
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
224
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
225
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
226 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:
7
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
227
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
228 BAM -> bamtools split => bcftools mpileup => bcftools call => bcftools concat -> VCF
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
229
d1ea6dede900 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a82f063287a78c9a237d1d0596b1176632581d42
iuc
parents: 5
diff changeset
230
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
231 @REGIONS_HELP@
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
232
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
233 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
234
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
235 @BCFTOOLS_HOWTOS@
9
50554a5bc884 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 7
diff changeset
236 ]]></help>
26
11c2dc7762b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 19
diff changeset
237 <expand macro="citations"/>
0
d4b771adb614 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff changeset
238 </tool>