Mercurial > repos > iuc > bcftools_mpileup

annotate bcftools_mpileup.xml @ 23:e1c8ab368943 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 08:00:58 +0000
parents 2f6e26a65721
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
1 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
2 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
3 <macros>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
4 <token name="@EXECUTABLE@">mpileup</token>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
5 <import>macros.xml</import>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
6 <xml name="bam_flag_options">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
7 <option value="1">Read is paired</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
8 <option value="2">Read is mapped in a proper pair</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
9 <option value="4">The read is unmapped</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
10 <option value="8">The mate is unmapped</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
11 <option value="16">Read strand</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
12 <option value="32">Mate strand</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
13 <option value="64">Read is the first in a pair</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
14 <option value="128">Read is the second in a pair</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
15 <option value="256">The alignment or this read is not primary</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
16 <option value="512">The read fails platform/vendor quality checks</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
17 <option value="1024">The read is a PCR or optical duplicate</option>
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
18 </xml>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
19 </macros>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
20 <expand macro="bio_tools"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
21 <expand macro="requirements">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
22 <expand macro="samtools_requirement"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
23 </expand>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
24 <expand macro="version_command"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
25 <command detect_errors="aggressive"><![CDATA[
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
26 #import re
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
27 #set bam_list = []
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
28 #if $input.input_number == 'single':
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
29 #set $input_base = $re.sub('\W','_',$input.input_bam.display_name.replace('.bam','').replace('.cram',''))
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
30 #set $ext = 'bam'
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
31 #set $idx_ext = 'bai'
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
32 #if $input.input_bam.ext == 'cram':
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
33 #set $ext = 'cram'
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
34 #set $idx_ext = 'crai'
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
35 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
36 #set $input_name = $input_base + '.' + $ext
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
37 #silent $bam_list.append($input_name)
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
38 ln -s '${input.input_bam}' ${input_name} &&
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
39 #if $input.input_bam.ext == 'bam':
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
40 ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
41 #else:
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
42 ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} &&
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
43 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
44 #else:
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
45 #for $bam_count, $input_bam in enumerate( $input.input_bams ):
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
46 #set $input_base = $re.sub('\W','_',$input_bam.display_name.replace('.bam','').replace('.cram',''))
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
47 #set $ext = 'bam'
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
48 #set $idx_ext = 'bai'
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
49 #if $input_bam.ext == 'cram':
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
50 #set $ext = 'cram'
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
51 #set $idx_ext = 'crai'
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
52 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
53 #set $input_name = $input_base + '.' + $ext
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
54 #silent $bam_list.append($input_name)
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
55 ln -s '${input_bam}' ${input_name} &&
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
56 ln -s '${input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
57 #end for
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
58 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
59
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
60 #set $input_fa_ref = None
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
61 #if $reference_source.reference_source_selector == "history":
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
62 #set $input_fa_ref = 'ref.fa'
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
63 ln -s '${reference_source.ref_file}' $input_fa_ref &&
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
64 samtools faidx $input_fa_ref &&
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
65 #elif $reference_source.reference_source_selector == "cached":
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
66 #set $input_fa_ref = $reference_source.ref_file.fields.path
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
67 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
68
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
69 #set $section = $sec_restrict
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
70 @PREPARE_REGIONS_FILE@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
71 @PREPARE_TARGETS_FILE@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
72
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
73 bcftools @EXECUTABLE@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
74
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
75 #if $input_fa_ref is not None:
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
76 --fasta-ref '$input_fa_ref'
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
77 #else:
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
78 --non-reference
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
79 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
80
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
81 ## Indel Calling section
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
82 #set $section = $sec_indel
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
83 #if $section.perform_indel_calling.perform_indel_calling_selector == 'do_not_perform_indel_calling':
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
84 --skip-indels
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
85 #elif $section.perform_indel_calling.perform_indel_calling_selector == 'perform_indel_calling':
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
86 -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}"
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
87 -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}"
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
88 -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
89 -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}"
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
90 -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
91 --open-prob "${section.perform_indel_calling.open_seq_error_probability}"
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
92 -F "${section.perform_indel_calling.minimum_gapped_read_fraction}"
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
93 ${section.perform_indel_calling.gapped_read_per_sample}
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
94 #if len( $section.perform_indel_calling.platform_list_repeat ):
20
4f3623db0d08 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5b9441b69b3c176ab7b89609495f66cb29d1091a
iuc
parents: 15
diff changeset
95 -P "${ ",".join( [ str( platform['platform_entry'] ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }"
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
96 #end if
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
97 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
98
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
99 #if $section.ambig_reads
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
100 --ambig-reads $section.ambig_reads
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
101 #end if
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
102
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
103 #if $section.indel_bias
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
104 --indel-bias $section.indel_bias
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
105 #end if
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
106
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
107 #if $section.indel_size
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
108 --indel-size $section.indel_size
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
109 #end if
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
110
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
111 ## Filter section
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
112 #set $section = $sec_filtering
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
113 #if str( $section.filter_by_flags.filter_flags ) == "filter":
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
114 #if $section.filter_by_flags.skip_all_set:
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
115 --skip-all-set ${sum([int(flag) for flag in str($section.filter_by_flags.skip_all_set).split(',')])}
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
116 #end if
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
117 #if $section.filter_by_flags.skip_any_set:
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
118 --skip-any-set ${sum([int(flag) for flag in str($section.filter_by_flags.skip_any_set).split(',')])}
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
119 #end if
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
120 #if $section.filter_by_flags.skip_all_unset:
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
121 --skip-all-unset ${sum([int(flag) for flag in str($section.filter_by_flags.skip_all_unset).split(',')])}
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
122 #end if
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
123 #if $section.filter_by_flags.skip_any_unset:
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
124 --skip-any-unset ${sum([int(flag) for flag in str($section.filter_by_flags.skip_any_unset).split(',')])}
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
125 #end if
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
126 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
127 -d "${section.max_reads_per_bam}"
14
fe142c9eae6c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 407e1d8f4dd1a60623783331926098f7f5624841
iuc
parents: 12
diff changeset
128 $section.ignore_overlaps
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
129 ${section.skip_anomalous_read_pairs}
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
130 #if str( $section.quality.quality_settings ) == "adjust":
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
131 $section.quality.baq
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
132 -q "${section.quality.minimum_mapping_quality}"
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
133 -Q "${section.quality.minimum_base_quality}"
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
134 -C "${section.quality.coefficient_for_downgrading}"
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
135 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
136 #if str( $section.read_groups.read_groups_selector ) == "ignore_rg":
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
137 --ignore-RG
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
138 #elif str( $section.read_groups.read_groups_selector ) == "paste":
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
139 -G "${section.read_groups.rg_action}${read_groups_file}"
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
140 #elif str( $section.read_groups.read_groups_selector ) == "history"
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
141 -G "${section.read_groups.rg_action}${section.read_groups.read_groups}"
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
142 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
143
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
144 #set $section = $sec_output_options
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
145 #if $section.output_tags:
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
146 --annotate "$section.output_tags"
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
147 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
148 #if $section.gvcf:
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
149 --gvcf "$section.gvcf"
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
150 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
151
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
152 ## Subset section
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
153 #set $section = $sec_subset
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
154 @SAMPLES@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
155
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
156 ## Restrict section
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
157 #set $section = $sec_restrict
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
158 @REGIONS@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
159 @TARGETS@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
160 @THREADS@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
161 @OUTPUT_TYPE@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
162
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
163 ## Primary Input/Outputs
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
164 #echo ' '.join($bam_list)#
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
165 > '$output_file'
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
166 #if str( $sec_filtering.read_groups.read_groups_selector ) == "paste":
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
167 && echo 'read-groups:'
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
168 && cat ${read_groups_file}
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
169 #end if
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
170 ]]></command>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
171 <configfiles>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
172 <configfile name="read_groups_file">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
173 <![CDATA[#slurp
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
174 #set pasted_data = ''
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
175 #set $section = $sec_filtering
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
176 #if str( $section.read_groups.read_groups_selector ) == "paste":
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
177 #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() )
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
178 #end if
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
179 #slurp
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
180 ${pasted_data}
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
181 ]]>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
182 </configfile>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
183 </configfiles>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
184 <inputs>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
185 <conditional name="input">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
186 <param name="input_number" type="select" label="Alignment Inputs">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
187 <option value="single">Single BAM/CRAM</option>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
188 <option value="multiple">Multiple BAM/CRAMs</option>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
189 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
190 <when value="single">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
191 <param name="input_bam" type="data" format="bam,cram" label="Input BAM/CRAM"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
192 </when>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
193 <when value="multiple">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
194 <param name="input_bams" type="data" format="bam,cram" multiple="true" label="Input BAM/CRAMs"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
195 </when>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
196 </conditional>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
197 <conditional name="reference_source">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
198 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
199 <option value="cached">Locally cached</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
200 <option value="history">History</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
201 <option value="none">No Reference</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
202 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
203 <when value="cached">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
204 <param name="ref_file" type="select" label="Select reference genome">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
205 <options from_data_table="fasta_indexes"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
206 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
207 </when>
22
2f6e26a65721 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 784611c9caf2680d41414ca2880b93a69d719701
iuc
parents: 20
diff changeset
208 <when value="history">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
209 <param name="ref_file" type="data" format="fasta" label="Genome Reference"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
210 </when>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
211 <when value="none"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
212 </conditional>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
213 <section name="sec_indel" expanded="false" title="Indel Calling">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
214 <conditional name="perform_indel_calling">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
215 <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
216 <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
217 <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
218 <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
219 </param>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
220 <when value="perform_indel_calling_def"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
221 <when value="perform_indel_calling">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
222 <param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="--open-prob; Reducing this value leads to more indel calls; default=40"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
223 <param name="gap_extension_sequencing_error_probability" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" help="--ext-prob; Reducing this value leads to longer indels. default=20"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
224 <param name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" label="Coefficient for modeling homopolymer errors." help="--tandem-qual; default=100"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
225 <param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" help="--max-idepth; default=250"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
226 <param name="minimum_gapped_reads_for_indel_candidates" type="integer" value="1" label="Minimum gapped reads for indel candidates" help="--min-ireads; default=1"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
227 <param name="open_seq_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="--open-prob; Reducing this value leads to more indel calls; default=40"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
228 <param name="minimum_gapped_read_fraction" type="float" value="0.002" label="Minimum fraction of gapped reads" help="--gap-frac; default=0.002"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
229 <param name="gapped_read_per_sample" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Apply --min-ireads and --gap-frac values on a per-sample basis" help="--per-sample-mF; by default both options are applied to reads pooled from all samples"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
230 <repeat name="platform_list_repeat" title="Platform for INDEL candidates">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
231 <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
232 </repeat>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
233 </when>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
234 <when value="do_not_perform_indel_calling"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
235 </conditional>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
236 <param argument="--ambig-reads" type="select" optional="true" label="Ambiguous indel reads" help="What to do with ambiguous indel reads that do not span an entire short tandem repeat region: discard ambiguous reads from calling and do not increment high-quality AD depth counters (drop), exclude from calling but increment AD counters proportionally (incAD), exclude from calling and increment the first value of the AD counter (incAD0) ">
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
237 <option value="drop">Drop</option>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
238 <option value="incAD">IncAD</option>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
239 <option value="incAD0">IncAD0</option>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
240 </param>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
241 <param argument="--indel-bias" type="float" min="0" value="" optional="true" label="Indel bias" help="Skews the indel scores up or down, trading recall (low false-negative) vs precision (low false-positive) [1.0]. In Bcftools 1.12 and earlier this parameter didn’t exist, but had an implied value of 1.0. If you are planning to do heavy filtering of variants, selecting the best quality ones only (favouring precision over recall), it is advisable to set this lower (such as 0.75) while higher depth samples or where you favour recall rates over precision may work better with a higher value such as 2.0"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
242 <param argument="--indel-size" type="integer" min="0" value="" optional="true" label="Indel size" help="Indel window size to use when assessing the quality of candidate indels. Note that although the window size approximately corresponds to the maximum indel size considered, it is not an exact threshold. Default: 110"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
243 </section>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
244 <section name="sec_filtering" expanded="false" title="Input Filtering Options">
12
bd0644ac3ab9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
iuc
parents: 10
diff changeset
245 <param name="max_reads_per_bam" type="integer" value="250" min="1" label="Max reads per BAM" help="--max-depth; default=250"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
246 <param name="ignore_overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" help="--ignore-overlaps"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
247 <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" help="--count-orphans"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
248 <conditional name="filter_by_flags">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
249 <param name="filter_flags" type="select" label="Set filter by flags">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
250 <option selected="True" value="nofilter">Do not filter</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
251 <option value="filter">Filter by flags to exclude or require</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
252 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
253 <when value="filter">
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
254 <param argument="--skip-all-set" type="select" display="checkboxes" label="Skip reads with all of the FLAG bits set" multiple="True" help="--skip-all-set">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
255 <expand macro="bam_flag_options"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
256 </param>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
257 <param argument="--skip-any-set" type="select" display="checkboxes" label="Skip reads with any of the FLAG bits set" multiple="True" help="--skip-any-set">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
258 <expand macro="bam_flag_options"/>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
259 </param>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
260 <param argument="--skip-all-unset" type="select" display="checkboxes" label="Skip reads with all of the FLAG bits unset" multiple="True" help="--skip-all-unset">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
261 <expand macro="bam_flag_options"/>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
262 </param>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
263 <param argument="--skip-any-unset" type="select" display="checkboxes" label="Skip reads with any of the FLAG bits unset" multiple="True" help="--skip-any-unset">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
264 <expand macro="bam_flag_options"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
265 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
266 </when>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
267 <when value="nofilter"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
268 </conditional>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
269 <conditional name="quality">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
270 <param label="Quality Options" name="quality_settings" type="select">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
271 <option value="none" selected="True">defaults</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
272 <option value="adjust">Set base and mapping quality options</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
273 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
274 <when value="adjust">
4
9a2923126c43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 3
diff changeset
275 <param name="baq" type="select" label="per-Base Alignment Quality">
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
276 <help>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
277 --no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments.
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
278 --redo-BAQ; ignore existing BQ tags
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
279 </help>
4
9a2923126c43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 3
diff changeset
280 <option value="">Default</option>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
281 <option value="--no-BAQ">disable BAQ (per-Base Alignment Quality) (no-BAQ)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
282 <option value="--redo-BAQ">recalculate BAQ on the fly, ignore existing BQs (redo-BAQ)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
283 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
284 <param name="coefficient_for_downgrading" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
285 <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
286 <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" help="--min-BQ; default=13"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
287 </when>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
288 <when value="none"/>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
289 </conditional>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
290 <conditional name="read_groups">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
291 <param name="read_groups_selector" type="select" label="Select read groups to include or exclude" help="--read-groups">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
292 <option value="no_limit" selected="True">use defaults</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
293 <option value="history">From an uploaded text file</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
294 <option value="paste">Paste a list of read groups</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
295 <option value="ignore_rg">Ignore RG tags. Treat all reads in one alignment file as one sample. </option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
296 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
297 <when value="history">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
298 <param name="read_groups" format="txt" label="Text file" type="data">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
299 <validator type="dataset_ok_validator"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
300 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
301 <param name="rg_action" type="select" label="Include or Exclude these Read Groups">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
302 <option value="" selected="true">Include</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
303 <option value="^">Exclude</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
304 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
305 </when>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
306 <when value="paste">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
307 <param name="group_paste" type="text" size="10x35" area="true" label="Read groups" help="Paste a list of read groups"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
308 <param name="rg_action" type="select" label="Include or Exclude these Read Groups">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
309 <option value="" selected="true">Include</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
310 <option value="^">Exclude</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
311 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
312 </when>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
313 <when value="ignore_rg"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
314 <when value="no_limit"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
315 </conditional>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
316 </section>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
317 <section name="sec_restrict" expanded="false" title="Restrict to">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
318 <expand macro="macro_region_restrict_simple"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
319 <expand macro="macro_target_restrict_simple"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
320 </section>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
321 <section name="sec_subset" expanded="false" title="Subset Options">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
322 <expand macro="macro_samples"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
323 </section>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
324 <section name="sec_output_options" expanded="false" title="Output options">
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
325 <expand macro="macro_output_tags">
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
326 <option value="DP">DP (Number of high-quality bases)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
327 <option value="AD">AD (Allelic depth)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
328 <option value="ADF">ADF (Allelic depth on the forward strand)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
329 <option value="ADR">ADR (Allelic depth on the reverse strand)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
330 <option value="INFO/AD">INFO/AD (Allelic depth)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
331 <option value="INFO/ADF">INFO/ADF (Allelic depth on the forward strand)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
332 <option value="INFO/ADR">INFO/ADR (Allelic depth on the reverse strand)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
333 <option value="SP">SP (Phred-scaled strand bias P-value)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
334 <option value="DV">DV (Number of high-quality non-reference bases)</option>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
335 <option value="QS">QS (Allele phred-score quality sum)</option>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
336 <option value="DP4">DP4 (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
337 <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
338 <option value="INFO/DPR">INFO/DPR (Number of high-quality bases for each observed allele)</option>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
339 </expand>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
340 <param name="gvcf" type="text" value="" label="gVCF blocks of homozygous REF calls">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
341 <help>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
342 output gVCF blocks of homozygous REF calls, with depth (DP) ranges specified by the list of integers. For example, passing 5,15 will group sites into two types of gVCF blocks, the first with minimum per-sample DP from the interval [5,15) and the latter with minimum depth 15 or more. In this example, sites with minimum per-sample depth less than 5 will be printed as separate records, outside of gVCF blocks.
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
343 </help>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
344 <validator type="regex" message="integers separated by commas">^(\d+(,\d+)*)?$</validator>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
345 </param>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
346 </section>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
347 <expand macro="macro_select_output_type"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
348 </inputs>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
349 <outputs>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
350 <expand macro="macro_vcf_output"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
351 </outputs>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
352 <tests>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
353 <test>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
354 <conditional name="input">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
355 <param name="input_number" value="single"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
356 <param name="input_bam" ftype="bam" value="mpileup.1.bam"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
357 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
358 <conditional name="reference_source">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
359 <param name="reference_source_selector" value="history"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
360 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
361 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
362 <param name="output_type" value="v"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
363 <output name="output_file">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
364 <assert_contents>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
365 <has_text text="mpileup"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
366 <has_text text="HG00100"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
367 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
368 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
369 </assert_contents>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
370 </output>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
371 </test>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
372 <test>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
373 <conditional name="input">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
374 <param name="input_number" value="single"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
375 <param name="input_bam" ftype="bam" value="mpileup.1.bam"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
376 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
377 <conditional name="reference_source">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
378 <param name="reference_source_selector" value="cached"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
379 <param name="ref_file" value="mpileup"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
380 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
381 <section name="sec_filtering">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
382 <conditional name="quality">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
383 <param name="quality_settings" value="adjust"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
384 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
385 </section>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
386 <param name="output_type" value="v"/>
4
9a2923126c43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 3
diff changeset
387 <output name="output_file">
9a2923126c43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 3
diff changeset
388 <assert_contents>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
389 <has_text text="mpileup"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
390 <has_text text="HG00100"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
391 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
392 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;"/>
4
9a2923126c43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 3
diff changeset
393 </assert_contents>
9a2923126c43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 3
diff changeset
394 </output>
9a2923126c43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 3
diff changeset
395 </test>
9a2923126c43 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 3
diff changeset
396 <test>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
397 <conditional name="input">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
398 <param name="input_number" value="single"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
399 <param name="input_bam" ftype="cram" value="mpileup.3.cram"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
400 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
401 <conditional name="reference_source">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
402 <param name="reference_source_selector" value="history"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
403 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
404 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
405 <param name="output_type" value="v"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
406 <output name="output_file">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
407 <assert_contents>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
408 <has_text text="mpileup"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
409 <has_text text="HG00102"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
410 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=5;"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
411 </assert_contents>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
412 </output>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
413 </test>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
414 <test>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
415 <conditional name="input">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
416 <param name="input_number" value="multiple"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
417 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
418 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
419 <conditional name="reference_source">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
420 <param name="reference_source_selector" value="history"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
421 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
422 </conditional>
5
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
423 <section name="sec_restrict">
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
424 <conditional name="regions">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
425 <param name="regions_src" value="regions"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
426 <repeat name="region_specs">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
427 <param name="chrom" value="17"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
428 <param name="start" value="100"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
429 <param name="stop" value="110"/>
5
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
430 </repeat>
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
431 </conditional>
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
432 </section>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
433 <section name="sec_output_options">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
434 <param name="output_tags" value="DP,INFO/AD,DV"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
435 </section>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
436 <param name="output_type" value="v"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
437 <output name="output_file">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
438 <assert_contents>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
439 <has_text text="mpileup"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
440 <has_text text="HG00100"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
441 <has_text text="HG00101"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
442 <has_text text="HG00102"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
443 <has_text text="ID=DP,"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
444 <not_has_text text="17\t111"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
445 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=18;AD=17,0;"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
446 </assert_contents>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
447 </output>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
448 </test>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
449 <test>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
450 <conditional name="input">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
451 <param name="input_number" value="multiple"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
452 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
453 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
454 <conditional name="reference_source">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
455 <param name="reference_source_selector" value="history"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
456 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
457 </conditional>
5
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
458 <section name="sec_restrict">
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
459 <conditional name="targets">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
460 <param name="targets_src" value="targets"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
461 <repeat name="target_specs">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
462 <param name="chrom" value="17"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
463 <param name="start" value="100"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
464 <param name="stop" value="104"/>
5
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
465 </repeat>
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
466 </conditional>
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
467 </section>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
468 <section name="sec_output_options">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
469 <param name="output_tags" value="DP,INFO/AD,DV"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
470 </section>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
471 <param name="output_type" value="v"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
472 <output name="output_file">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
473 <assert_contents>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
474 <has_text text="mpileup"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
475 <has_text text="HG00100"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
476 <has_text text="HG00101"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
477 <has_text text="HG00102"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
478 <has_text text="ID=DP,"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
479 <not_has_text text="17\t105"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
480 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=18;AD=17,0;"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
481 </assert_contents>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
482 </output>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
483 </test>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
484 <test>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
485 <conditional name="input">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
486 <param name="input_number" value="multiple"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
487 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
488 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
489 <conditional name="reference_source">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
490 <param name="reference_source_selector" value="history"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
491 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
492 </conditional>
5
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
493 <section name="sec_restrict">
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
494 <conditional name="regions">
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
495 <param name="regions_src" value="regions"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
496 <repeat name="region_specs">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
497 <param name="chrom" value="17"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
498 <param name="start" value="1050"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
499 <param name="stop" value="1060"/>
5
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
500 </repeat>
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
501 </conditional>
0bf290bc84ae planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 4
diff changeset
502 </section>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
503 <section name="sec_filtering">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
504 <conditional name="filter_by_flags">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
505 <param name="filter_flags" value="filter"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
506 <param name="skip_all_set" value="4,16"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
507 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
508 </section>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
509 <param name="output_type" value="v"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
510 <output name="output_file">
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
511 <assert_contents>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
512 <has_text text="mpileup"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
513 <has_text text="HG00100"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
514 <has_text_matching expression="17\t1050\t.\tA\t"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
515 </assert_contents>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
516 </output>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
517 <assert_command>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
518 <has_text text="--skip-all-set"/>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
519 </assert_command>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
520 </test>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
521 <!-- Test indel options-->
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
522 <test>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
523 <conditional name="input">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
524 <param name="input_number" value="single"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
525 <param name="input_bam" ftype="bam" value="mpileup.1.bam"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
526 </conditional>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
527 <conditional name="reference_source">
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
528 <param name="reference_source_selector" value="history"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
529 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
530 </conditional>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
531 <section name="sec_indel">
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
532 <param name="ambig_reads" value="drop"/>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
533 <param name="indel_bias" value="1"/>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
534 <param name="indel_size" value="110"/>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
535 </section>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
536 <param name="output_type" value="v"/>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
537 <output name="output_file">
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
538 <assert_contents>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
539 <has_text text="mpileup"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
540 <has_text text="HG00100"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
541 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
542 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;"/>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
543 </assert_contents>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
544 </output>
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
545 <assert_command>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
546 <has_text text="--ambig-reads"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
547 <has_text text="--indel-bias"/>
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
548 <has_text text="--indel-size"/>
15
d8a653c52f61 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 14
diff changeset
549 </assert_command>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
550 </test>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
551 </tests>
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
552 <help><![CDATA[
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
553 =====================================
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
554 bcftools @EXECUTABLE@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
555 =====================================
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
556
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
557 Haplotype aware consequence predictor which correctly handles combined variants such as MNPs split over multiple VCF records, SNPs separated by an intron (but adjacent in the spliced transcript) or nearby frame-shifting indels which in combination in fact are not frame-shifting.
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
558
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
559 The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c option). The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See the usage examples below for using the %TBCSQ converter in query for extracting a more human readable form from this bitmask. The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags. By default this is 16, but if more are required, see the --ncsq option.
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
560
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
561 The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref) and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot), and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported.
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
562
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
563 By default, the input VCF should be phased. If phase is unknown, or only partially known, the --phase option can be used to indicate how to handle unphased data. Alternatively, haplotype aware calling can be turned off with the --local-csq option.
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
564
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
565 If conflicting (overlapping) variants within one haplotype are detected, a warning will be emitted and predictions will be based on only the first variant in the analysis.
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
566
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
567 Symbolic alleles are not supported. They will remain unannotated in the output VCF and are ignored for the prediction analysis.
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
568
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
569
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
570 @REGIONS_HELP@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
571 @TARGETS_HELP@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
572
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
573 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
574
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
575 @BCFTOOLS_HOWTOS@
3
4422d017fe79 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
iuc
parents: 0
diff changeset
576 ]]></help>
23
e1c8ab368943 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools commit f6efda26965eb73c9107d367fd5ffdf246ed0dbc
iuc
parents: 22
diff changeset
577 <expand macro="citations"/>
0
d29cba4286a5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 10853682ffb2e9776256bb63c899ef5c5fe0007e
iuc
parents:
diff changeset
578 </tool>