Mercurial > repos > devteam > freebayes

annotate freebayes.xml @ 21:cbacfc763eb0 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/master/tools/freebayes commit c02672d4d8da0419efa4a13290ba628b4eee8304
author iuc
date Tue, 10 Jun 2025 07:59:38 +0000
parents ed8508ec9613
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
21
cbacfc763eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit c02672d4d8da0419efa4a13290ba628b4eee8304
iuc
parents: 20
diff changeset
1 <tool id="freebayes" name="FreeBayes" version="@TOOL_VERSION@+galaxy0">
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
2 <description>bayesian genetic variant detector</description>
12
2667d6a97b50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 11
diff changeset
3 <xrefs>
2667d6a97b50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 11
diff changeset
4 <xref type="bio.tools">freebayes</xref>
2667d6a97b50 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 11
diff changeset
5 </xrefs>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
6 <macros>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
7 <import>macros.xml</import>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
8 </macros>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
9 <expand macro="requirements">
18
37da353c7689 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit fe6bd492e3188ec78ef4bc5111c5da40eae05b0a
iuc
parents: 16
diff changeset
10 <requirement type="package" version="5.3.1">gawk</requirement>
21
cbacfc763eb0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit c02672d4d8da0419efa4a13290ba628b4eee8304
iuc
parents: 20
diff changeset
11 <requirement type="package" version="20250422">parallel</requirement>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
12 </expand>
16
a2feedafda6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit be1c2e9e056710ef8b1110a121dc38c6e06dbbee"
iuc
parents: 15
diff changeset
13 <expand macro="version_command" />
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
14 <command detect_errors="exit_code"><![CDATA[
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
15 ##set up input files
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
16
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
17 #set $reference_fasta_filename = "localref.fa"
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
18
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
19 #if str( $reference_source.reference_source_selector ) == "history":
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
20 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
21 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
22 #else:
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
23 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
24 #end if
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
25
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
26 #if $reference_source.batchmode.processmode == 'merge':
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
27 #set $input_bamfiles = $reference_source.batchmode.input_bams
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
28 #else:
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
29 #set $input_bamfiles = [ $reference_source.batchmode.input_bams ]
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
30 #end if
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
31
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
32 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
33 #if $input_bam.ext == 'bam':
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
34 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
35 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
36 #elif $input_bam.ext == 'cram':
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
37 ln -s -f '${input_bam}' 'b_${bam_count}.cram' &&
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
38 ln -s -f '${input_bam.metadata.cram_index}' 'b_${bam_count}.cram.crai' &&
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
39 #end if
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
40 #end for
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
41
20
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
42 ## For --variant-input option, create symlinks to vcf.bgzip input and its accompanying tabix index
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
43 #if ( str( $options_type.options_type_selector ) == 'cline' or str( $options_type.options_type_selector ) == 'full' ) and str( $options_type.optional_inputs.optional_inputs_selector ) == 'set' and str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
44 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' input_variant_vcf.vcf.gz &&
20
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
45 ln -s '$options_type.optional_inputs.input_variant_type.input_variant_vcf.metadata.tabix_index' input_variant_vcf.vcf.gz.tbi &&
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
46 #end if
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
47
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
48 ##if the user has specified a region or target file, just use that instead of calculating a set of unique regions
7
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
parents: 6
diff changeset
49 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
parents: 6
diff changeset
50 ln -s '${target_limit_type.input_target_bed}' regions_all.bed &&
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
parents: 6
diff changeset
51 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
parents: 6
diff changeset
52 printf '${target_limit_type.region_chromosome}\t${target_limit_type.region_start}\t${target_limit_type.region_end}' > regions_all.bed &&
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
parents: 6
diff changeset
53 #else
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
parents: 6
diff changeset
54 ##divide up the regions in the bam file for efficient processing
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
55 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
56 samtools view -H b_${bam_count}.${input_bam.ext}|
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
57 grep '^@SQ' |
7
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
parents: 6
diff changeset
58 cut -f 2- |
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
59 awk '{ gsub("^SN:","",$1); gsub("^LN:","",$2); print $1"\t0\t"$2; }' >> regions_all.bed &&
7
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
parents: 6
diff changeset
60 #end for
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
parents: 6
diff changeset
61 #end if
d0997bd93c49 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 0c59a0b32e4875120e697951a187b81c662bc39c
iuc
parents: 6
diff changeset
62
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
63 sort -u regions_all.bed > regions_uniq.bed &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
64 ## split into even small chunks, this has some disatvantages and will not be used for the moment
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
65 ## bedtools makewindows -b regions_uniq.bed -w 10000000 -s 9990000 > regions.bed &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
66
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
67 mkdir vcf_output failed_alleles trace &&
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
68
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
69 ## Finished setting up inputs
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
70
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
71 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
72 do
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
73 echo "
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
74
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
75 ## COMMAND LINE STARTS HERE
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
76
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
77 freebayes
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
78
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
79 --region '\$i'
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
80
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
81 #for $bam_count, $input_bam in enumerate( $input_bamfiles ):
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
82 --bam 'b_${bam_count}.${input_bam.ext}'
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
83 #end for
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
84 --fasta-reference '${reference_fasta_filename}'
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
85
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
86 ## Outputs
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
87 --vcf './vcf_output/part_\$i.vcf'
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
88
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
89 ## Coverage
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
90 #if str($coverage_options.coverage_options_selector) == "set":
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
91 @COVERAGE@
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
92 #end if
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
93
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
94 ##advanced options
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
95 #if str( $options_type.options_type_selector ) == "simple":
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
96 #pass
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
97 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
98 --standard-filters
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
99 #elif str( $options_type.options_type_selector ) == "naive":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
100 --haplotype-length 0
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
101 --min-alternate-count 1
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
102 --min-alternate-fraction 0.05
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
103 --pooled-continuous
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
104 --report-monomorphic
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
105 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
106 --haplotype-length 0
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
107 --min-alternate-count 1
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
108 --min-alternate-fraction 0.05
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
109 --pooled-continuous
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
110 --report-monomorphic
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
111 --standard-filters
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
112 #elif str( $options_type.options_type_selector ) == "full":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
113 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
114 ${options_type.optional_inputs.report_monomorphic}
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
115
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
116 #if $options_type.optional_inputs.output_trace_option:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
117 --trace ./trace/part_'\$i'.txt
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
118 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
119 #if $options_type.optional_inputs.output_failed_alleles_option:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
120 --failed-alleles ./failed_alleles/part_'\$i'.bed
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
121 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
122 #if $options_type.optional_inputs.samples:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
123 --samples '${options_type.optional_inputs.samples}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
124 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
125 #if $options_type.optional_inputs.populations:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
126 --populations '${options_type.optional_inputs.populations}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
127 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
128 #if $options_type.optional_inputs.A:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
129 --cnv-map '${options_type.optional_inputs.A}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
130 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
131 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
20
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
132 --variant-input 'input_variant_vcf.vcf.gz'
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
133 ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
134 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
135 #if $options_type.optional_inputs.haplotype_basis_alleles:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
136 --haplotype-basis-alleles '${options_type.optional_inputs.haplotype_basis_alleles}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
137 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
138 #if $options_type.optional_inputs.observation_bias:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
139 --observation-bias '${options_type.optional_inputs.observation_bias}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
140 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
141 #if $options_type.optional_inputs.contamination_estimates:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
142 --contamination-estimates '${options_type.optional_inputs.contamination_estimates}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
143 #end if
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
144 $options_type.optional_inputs.trim_complex_tail
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
145 #end if
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
146
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
147 ## REPORTING
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
148 #if str( $options_type.reporting.reporting_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
149 --pvar ${options_type.reporting.pvar}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
150 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
151 ## POPULATION MODEL
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
152 #if str( $options_type.population_model.population_model_selector ) == "set":
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
153 --theta ${options_type.population_model.T}
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
154 --ploidy ${options_type.population_model.P}
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
155 ${options_type.population_model.J}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
156 ${options_type.population_model.K}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
157 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
158
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
159 ## REFERENCE ALLELE
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
160 #if str( $options_type.reference_allele.reference_allele_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
161 ${options_type.reference_allele.Z}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
162 --reference-quality '${options_type.reference_allele.reference_quality}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
163 #end if
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
164
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
165 ## ALLELE SCOPE
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
166 #if str( $options_type.allele_scope.allele_scope_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
167 ${options_type.allele_scope.I}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
168 ${options_type.allele_scope.i}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
169 ${options_type.allele_scope.X}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
170 ${options_type.allele_scope.u}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
171 ${options_type.allele_scope.no_partial_observations}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
172
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
173 -n ${options_type.allele_scope.n}
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
174
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
175 --haplotype-length ${options_type.allele_scope.haplotype_length}
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
176 --min-repeat-size ${options_type.allele_scope.min_repeat_length}
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
177 --min-repeat-entropy ${options_type.allele_scope.min_repeat_entropy}
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
178 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
179
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
180 ## REALIGNMENT
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
181 ${options_type.O}
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
182
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
183 ##INPUT FILTERS
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
184 #if str( $options_type.input_filters.input_filters_selector ) == "set":
15
c3da1614f96d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit a89c26123a658a71af5a0a66245b977384ab8867"
iuc
parents: 14
diff changeset
185 ${options_type.input_filters.standard_filters}
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
186 ${options_type.input_filters.use_duplicate_reads}
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
187 --min-mapping-quality ${options_type.input_filters.min_mapping_quality}
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
188 --min-base-quality ${options_type.input_filters.min_base_quality}
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
189 --min-supporting-allele-qsum ${options_type.input_filters.min_supporting_allele_qsum}
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
190 --min-supporting-mapping-qsum ${options_type.input_filters.min_supporting_mapping_qsum}
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
191 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
192 --mismatch-base-quality-threshold ${options_type.input_filters.mismatch_filters.mismatch_base_quality_threshold}
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
193 #if str($options_type.input_filters.mismatch_filters.read_mismatch_limit)
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
194 --read-mismatch-limit ${options_type.input_filters.mismatch_filters.read_mismatch_limit}
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
195 #end if
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
196 --read-max-mismatch-fraction ${options_type.input_filters.mismatch_filters.read_max_mismatch_fraction}
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
197 --read-snp-limit ${options_type.input_filters.mismatch_filters.read_snp_limit}
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
198 #end if
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
199 --read-indel-limit ${options_type.input_filters.read_indel_limit}
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
200 --min-alternate-fraction ${options_type.input_filters.min_alternate_fraction}
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
201 --min-alternate-qsum ${options_type.input_filters.min_alternate_qsum}
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
202 --min-alternate-count ${options_type.input_filters.min_alternate_count}
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
203 --min-alternate-total ${options_type.input_filters.min_alternate_total}
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
204 #end if
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
205
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
206 ## POPULATION AND MAPPABILITY PRIORS
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
207 #if str( $options_type.population_mappability_priors.population_mappability_priors_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
208 ${options_type.population_mappability_priors.k}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
209 ${options_type.population_mappability_priors.w}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
210 ${options_type.population_mappability_priors.V}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
211 ${options_type.population_mappability_priors.a}
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
212 #end if
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
213
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
214 ## GENOTYPE LIKELIHOODS
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
215 #if str( $options_type.genotype_likelihoods.genotype_likelihoods_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
216 ${$options_type.genotype_likelihoods.experimental_gls}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
217
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
218 --base-quality-cap ${$options_type.genotype_likelihoods.base_quality_cap}
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
219 --prob-contamination ${$options_type.genotype_likelihoods.prob_contamination}
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
220 #end if
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
221
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
222 ## ALGORITHMIC FEATURES
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
223 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
224 -B '${options_type.algorithmic_features.B}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
225 -W '${options_type.algorithmic_features.W}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
226 -D '${options_type.algorithmic_features.D}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
227
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
228 #if str($options_type.algorithmic_features.genotype_variant_threshold)
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
229 -S ${options_type.algorithmic_features.genotype_variant_threshold}
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
230 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
231
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
232 ${options_type.algorithmic_features.N}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
233 ${options_type.algorithmic_features.j}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
234 ${options_type.algorithmic_features.H}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
235 ${options_type.algorithmic_features.genotype_qualities}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
236 ${options_type.algorithmic_features.report_genotype_likelihood_max}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
237
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
238 --genotyping-max-banddepth ${options_type.algorithmic_features.genotyping_max_banddepth}
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
239 #end if
3
9f3d6c3098ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents: 2
diff changeset
240 #end if
9f3d6c3098ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents: 2
diff changeset
241
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
242 ";
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
243 done > freebayes_commands.sh &&
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
244
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
245 cat freebayes_commands.sh |
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
246 parallel --will-cite -j \${GALAXY_SLOTS:-1} &&
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
247
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
248 ## make VCF header
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
249 grep "^#" "./vcf_output/part_\$i.vcf" > header.txt &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
250
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
251 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
252 do
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
253 ## if this fails then it bails out the script
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
254 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
255 ;
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
256 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
257
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
258 #if str( $options_type.options_type_selector ) == "full":
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
259 #if str( $options_type.optional_inputs.optional_inputs_selector ) == 'set':
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
260 #if $options_type.optional_inputs.output_failed_alleles_option:
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
261 &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
262 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
263 do
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
264 cat "./failed_alleles/part_\$i.bed"
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
265 ;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
266 done > '${output_failed_alleles_bed}'
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
267 #end if
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
268
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
269 #if $options_type.optional_inputs.output_trace_option:
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
270 &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
271 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
272 do
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
273 cat './trace/part_\$i.txt'
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
274 ;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
275 done > '${output_trace}'
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
276 #end if
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
277 #end if
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
278 #end if
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
279 ]]></command>
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
280
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
281 <inputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
282 <conditional name="reference_source">
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
283 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
284 <option value="cached">Locally cached</option>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
285 <option value="history">History</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
286 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
287 <when value="cached">
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
288 <expand macro="input_bam">
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
289 <expand macro="validation" />
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
290 </expand>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
291 <param name="ref_file" type="select" label="Using reference genome">
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
292 <options from_data_table="fasta_indexes" />
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
293 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input dataset"/>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
294 </param>
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
295 </when>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
296 <when value="history"> <!-- FIX ME!!!! -->
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
297 <expand macro="input_bam" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
298 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
299 help="You can upload a FASTA sequence to the history and use it as reference" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
300 </when>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
301 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
302 <conditional name="target_limit_type">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
303 <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
304 <option value="do_not_limit" selected="true">Do not limit</option>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
305 <option value="limit_by_target_file">Limit by target file</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
306 <option value="limit_by_region">Limit to region</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
307 </param>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
308 <when value="do_not_limit" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
309 <when value="limit_by_target_file">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
310 <param name="input_target_bed" argument="--targets" type="data" format="bed" label="Limit analysis to regions in this BED dataset" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
311 </when>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
312 <when value="limit_by_region">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
313 <param name="region_chromosome" argument="--region" type="text" label="Region Chromosome" value="" /> <!--only once? -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
314 <param name="region_start" type="integer" label="Region Start" value="" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
315 <param name="region_end" type="integer" label="Region End" value="" />
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
316 </when>
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
317 </conditional>
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
318 <conditional name="coverage_options">
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
319 <param name="coverage_options_selector" type="select" label="Read coverage"
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
320 help="Sets --min-coverage, --limit-coverage, and --skip-coverage">
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
321 <option value="do_not_set" selected="true">Use defaults</option>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
322 <option value="set">Specify coverage options</option>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
323 </param>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
324 <when value="set">
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
325 <expand macro="par_min_cov" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
326 </when>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
327 <when value="do_not_set" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
328 </conditional>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
329 <conditional name="options_type">
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
330 <param name="options_type_selector" type="select" label="Choose parameter selection level"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
331 help="Select how much control over the freebayes run you need">
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
332 <option value="simple" selected="true">1. Simple diploid calling</option>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
333 <option value="simple_w_filters">2. Simple diploid calling with filtering and coverage</option>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
334 <option value="naive">3. Frequency-based pooled calling</option>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
335 <option value="naive_w_filters">4. Frequency-based pooled calling with filtering and coverage</option>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
336 <option value="full">5. Full list of options</option>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
337 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
338 <when value="full">
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
339
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
340 <conditional name="optional_inputs">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
341 <param name="optional_inputs_selector" type="select" label="Additional inputs"
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
342 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --variant-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, --contamination-estimates and --trim-complex-tail">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
343 <option value="do_not_set" selected="true">Do not provide additional inputs</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
344 <option value="set">Provide additional inputs</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
345 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
346 <when value="set">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
347 <param name="output_failed_alleles_option" argument="--failed-alleles" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
348 label="Write out failed alleles file" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
349 <param name="output_trace_option" argument="--trace" type="boolean" truevalue="--trace" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
350 label="Write out algorithm trace file" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
351 <param argument="--samples" type="data" format="txt"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
352 label="Limit analysis to samples listed (one per line) in this dataset" optional="true"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
353 help="By default FreeBayes will analyze all samples in its input BAM datasets" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
354 <param argument="--populations" type="data" format="txt" optional="true"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
355 label="Populations dataset"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
356 help="Each line of this dataset should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
357 <param name="A" argument="--cnv-map" type="data" format="bed" optional="true"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
358 label="Read a copy number map from a BED dataset"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
359 help="The BED dataset should have the format: 'reference sequence, start, end, sample name, copy number' for each region in each sample which does not have the default copy number as set by --ploidy. If not specified, copy number is set to as specified by --ploidy" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
360 <conditional name="input_variant_type">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
361 <param name="input_variant_type_selector" type="select" label="Provide variants dataset">
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
362 <option value="do_not_provide" selected="true">Do not provide</option>
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
363 <option value="provide_vcf">Provide VCF dataset</option>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
364 </param>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
365 <when value="do_not_provide" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
366 <when value="provide_vcf">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
367 <param name="input_variant_vcf" argument="--variant-input" type="data" format="vcf_bgzip"
20
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
368 label="Use variants reported in this VCF dataset as input to the algorithm"/>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
369 <param name="only_use_input_alleles" argument="--only-use-input-alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
370 label="Only provide variant calls and genotype likelihoods for sites in VCF" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
371 </when>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
372 </conditional>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
373 <param name="haplotype_basis_alleles" argument="--haplotype-basis-alleles" type="data" format="vcf" optional="true"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
374 label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
375 <param name="report_monomorphic" argument="--report-monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
376 label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
377 <param name="observation_bias" argument="--observation-bias" type="data" format="tabular" optional="true"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
378 label="Load read length-dependent allele observation biases from"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
379 help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
380 <param name="contamination_estimates" argument="--contamination-estimates" type="data" format="tabular" optional="true"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
381 label="Upload per-sample estimates of contamination from"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
382 help="The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates" />
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
383 <param name="trim_complex_tail" argument="--trim-complex-tail" type="boolean" truevalue="--trim-complex-tail" falsevalue=""
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
384 label="Trim trailing reference matches" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
385 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
386 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
387 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
388
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
389 <!-- reporting -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
390 <conditional name="reporting">
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
391 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
392 <option value="do_not_set" selected="true">Use defaults</option>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
393 <option value="set">Set reporting options</option>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
394 </param>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
395 <when value="set">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
396 <param argument="--pvar" type="float" value="0.0"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
397 label="Report sites if the probability that there is a polymorphism at the site is greater than"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
398 help="Note that post-filtering is generally recommended over the use of this parameter" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
399 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
400 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
401 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
402
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
403 <!-- population model -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
404 <conditional name="population_model">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
405 <param name="population_model_selector" type="select" label="Population model options"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
406 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
407 <option value="do_not_set" selected="true">Use defaults</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
408 <option value="set">Set population model options</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
409 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
410 <when value="set">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
411 <param name="T" argument="--theta" type="float" value="0.001"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
412 label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
413 help="This serves as the single parameter to the Ewens Sampling Formula prior model" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
414 <param name="P" argument="--ploidy" type="integer" value="2"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
415 label="Set ploidy for the analysis" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
416 <param name="J" argument="--pooled-discrete" type="boolean" truevalue="-J" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
417 label="Assume that samples result from pooled sequencing"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
418 help="Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
419 <param name="K" argument="--poled-continuous" type="boolean" truevalue="-K" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
420 label="Output all alleles which pass input filters, regardles of genotyping outcome or model" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
421 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
422 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
423 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
424
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
425 <!-- reference allele -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
426 <conditional name="reference_allele">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
427 <param name="reference_allele_selector" type="select" label="Reference allele options"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
428 help="Sets --use-reference-allele and --reference-quality options">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
429 <option value="do_not_set" selected="true">Use defaults</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
430 <option value="set">Set reference allele options</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
431 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
432 <when value="set">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
433 <param name="Z" argument="--use-reference-allele" type="boolean" truevalue="-Z" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
434 label="Include the reference allele in the analysis as if it is another sample from the same population" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
435 <param name="reference_quality" argument="--reference-quality" type="text" value="100,60"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
436 label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
437 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
438 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
439 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
440
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
441 <!-- allelic scope -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
442 <conditional name="allele_scope">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
443 <param name="allele_scope_selector" type="select" label="Allelic scope options"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
444 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
445 <option value="do_not_set" selected="true">Use defaults</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
446 <option value="set">Set alleic scope options</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
447 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
448 <when value="set">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
449 <param name="I" argument="--no-snps" type="boolean" truevalue="-I" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
450 label="Ignore SNP alleles" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
451 <param name="i" argument="--no-indels" type="boolean" truevalue="-i" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
452 label="Ignore indels alleles" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
453 <param name="X" argument="--no-mnps" type="boolean" truevalue="-X" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
454 label="Ignore multi-nucleotide polymorphisms, MNPs" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
455 <param name="u" argument="--no-complex" type="boolean" truevalue="-u" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
456 label="Ignore complex events (composites of other classes)" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
457 <param name="n" argument="--use-best-n-alleles" type="integer" value="0"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
458 label="How many best SNP alleles to evaluate"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
459 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
460 <param name="haplotype_length" argument="--haplotype-length" type="integer" value="3"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
461 label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
462 <param name="min_repeat_length" argument="--min-repeat-size" type="integer" value="5"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
463 label="When assembling observations across repeats, require the total repeat length at least this many bp" />
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
464 <param name="min_repeat_entropy" argument="--min-repeat-entropy" type="integer" value="1"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
465 label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
466 <param name="no_partial_observations" argument="--no-partial-observations" type="boolean" truevalue="--no-partial-observations" falsevalue="" checked="false"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
467 label="Exclude observations which do not fully span the dynamically-determined detection window"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
468 help="By default, FreeBayes uses all observations, dividing partial support across matching haplotypes when generating haplotypes" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
469 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
470 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
471 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
472
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
473 <!-- indel realignment -->
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
474 <param name="O" argument="--dont-left-align-indels" type="boolean" truevalue="-O" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
475 label="Turn off left-alignment of indels" />
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
476
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
477 <!-- input filters -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
478 <conditional name="input_filters">
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
479 <param name="input_filters_selector" type="select" label="Input filters">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
480 <option value="do_not_set" selected="true">No input filters (default)</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
481 <option value="set">Set input filters</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
482 </param>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
483 <when value="set">
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
484 <param argument="--standard-filters" type="boolean" truevalue="--standard-filters" falsevalue="" checked="false"
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
485 label="Use stringent input base and mapping quality filters"
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
486 help="--min-mapping-quality 30 --min-base-quality 20, --min-supporting-allele-qsum 0 --genotype-variant-threshold 0"/>
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
487 <param argument="--use-duplicate-reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="false"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
488 label="Include duplicate-marked alignments in the analysis" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
489 <param argument="--min-mapping-quality" type="integer" value="1"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
490 label="Exclude alignments from analysis if they have a mapping quality less than" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
491 <param argument="--min-base-quality" type="integer" value="0"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
492 label="Exclude alleles from analysis if their supporting base quality less than" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
493 <param argument="--min-supporting-allele-qsum" type="integer" value="0"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
494 label="Consider any allele in which the sum of qualities of supporting observations is at least" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
495 <param argument="--min-supporting-mapping-qsum" type="integer" value="0"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
496 label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
497 <conditional name="mismatch_filters">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
498 <param name="mismatch_filters_selector" type="select" label="Mismatch filters"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
499 help="Sets -Q, -U, -z, and &#36; options">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
500 <option value="do_not_set" selected="true">No mismatch filters (default)</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
501 <option value="set">Set mismatch filters</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
502 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
503 <when value="set">
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
504 <param argument="--mismatch-base-quality-threshold" type="integer" value="10"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
505 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >=" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
506 <param argument="--read-mismatch-limit" type="integer" value="1000" optional="true"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
507 label="Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (option above)"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
508 help="default=~unbounded" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
509 <param argument="--read-max-mismatch-fraction" type="float" value="1.0" min="0.0" max="1.0"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
510 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold (second option above)" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
511 <param name="read_snp_limit" argument="--read-snp-limit" type="integer" value="1000"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
512 label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold (third option above)"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
513 help="default=~unbounded" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
514 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
515 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
516 </conditional>
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
517 <param argument="--read-indel-limit" type="integer" value="1000"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
518 label="Exclude reads with more than this number of separate gaps"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
519 help="default=~unbounded" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
520 <param argument="--min-alternate-fraction" type="float" value="0.05"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
521 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
522 <param argument="--min-alternate-qsum" type="integer" value="0"
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
523 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" />
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
524 <param argument="--min-alternate-count" type="integer" value="2"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
525 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" />
13
5031b6656a2b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 3b5abd63372c2806870627e9dc2a2f0f52f2e52a"
iuc
parents: 12
diff changeset
526 <param argument="--min-alternate-total" type="integer" value="1"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
527 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
528 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
529 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
530 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
531
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
532 <!-- population and mappability priors -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
533 <conditional name="population_mappability_priors">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
534 <param name="population_mappability_priors_selector" type="select" label="Population and mappability priors"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
535 help="Sets -k, -w, -V, and -a options">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
536 <option value="do_not_set" selected="true">Use defaults</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
537 <option value="set">Set population and mappability priors</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
538 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
539 <when value="set">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
540 <param name="k" argument="--no-population-priors" type="boolean" truevalue="-k" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
541 label="No population priors"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
542 help="Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
543 <param name="w" argument="--hwe-priors-off" type="boolean" truevalue="-w" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
544 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
545 <param name="V" argument="--binomial-obs-priors-off" type="boolean" truevalue="-V" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
546 label="Disable incorporation of prior expectations about observations"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
547 help="Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
548 <param name="a" argument="--allele-balance-priors-off" type="boolean" truevalue="-a" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
549 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
550 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
551 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
552 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
553
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
554 <!-- genotype likelihoods -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
555 <conditional name="genotype_likelihoods">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
556 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
557 help="Sets --base-quality-cap, --experimental-gls, and --prob-contamination options">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
558 <option value="do_not_set" selected="true">Use defaults</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
559 <option value="set">Set genotype likelihood options</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
560 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
561 <when value="set">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
562 <param name="base_quality_cap" argument="--base-quality-cap" type="integer" value="0"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
563 label="Limit estimated observation quality by capping base quality at" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
564 <param name="experimental_gls" argument="--experimental-gls" type="boolean" truevalue="--experimental-gls" falsevalue="" checked="false"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
565 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
566 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
567 <param name="prob_contamination" argument="--prob-contamination" type="float" value="10e-9"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
568 label="An estimate of contamination to use for all samples" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
569 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
570 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
571 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
572
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
573 <!-- algorithmic features -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
574 <conditional name="algorithmic_features">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
575 <param name="algorithmic_features_selector" type="select" label="Algorithmic features"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
576 help="Sets --report-genotypes-likelihood-max, -B, --genotyping-max-banddepth, -W, -N, S, -j, -H, -D, -= options">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
577 <option value="do_not_set" selected="true">Use defaults</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
578 <option value="set">Set algorithmic features</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
579 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
580 <when value="set">
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
581 <param name="report_genotype_likelihood_max" argument="--report-genotype-likelihood-max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
582 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
583 <param name="B" argument="--genotyping-max-iterations" type="integer" value="1000"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
584 label="Iterate no more than N times during genotyping step" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
585 <param name="genotyping_max_banddepth" argument="--genotyping-max-banddepth" type="integer" value="6"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
586 label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
587 <param name="W" argument="--posterior-integration-limits" type="text" value="1,3"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
588 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
589 <param name="N" argument="--exclude-unobserved-genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
590 label="Skip sample genotypings for which the sample has no supporting reads" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
591 <param name="genotype_variant_threshold" argument="--genotype-variant-threshold" type="integer" value="" optional="true"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
592 label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
593 help="default=~unbounded" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
594 <param name="j" argument="--use-mapping-quality" type="boolean" truevalue="-j" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
595 label="Use mapping quality of alleles when calculating data likelihoods" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
596 <param name="H" argument="--harmonic-indel-quality" type="boolean" truevalue="-H" falsevalue="" checked="false"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
597 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
598 help="By default, FreeBayes uses a minimum Base Quality in flanking sequence" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
599 <param name="D" argument="--read-dependence-factor" type="float" value="0.9"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
600 label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" />
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
601 <param name="genotype_qualities" argument="--genotype-qualities" type="boolean" truevalue="--genotype-qualities" falsevalue="" checked="false"
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
602 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
603 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
604 <when value="do_not_set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
605 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
606 </when>
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
607 <when value="simple" />
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
608 <when value="simple_w_filters" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
609 <when value="naive" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
610 <when value="naive_w_filters" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
611 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
612 </inputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
613 <outputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
614 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
615 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
616 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
617 </data>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
618 <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
619 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_trace_option'] is True</filter>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
620 </data>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
621 </outputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
622 <tests>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
623 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
624 <param name="reference_source_selector" value="history" />
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
625 <param name="processmode" value="individual" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
626 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
627 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
628 <param name="options_type_selector" value="simple"/>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
629 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
630 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
631 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
632 <param name="reference_source_selector" value="history" />
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
633 <param name="processmode" value="individual" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
634 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
635 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
636 <param name="options_type_selector" value="naive_w_filters"/>
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
637 <param name="coverage_options_selector" value="set" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
638 <param name="min_coverage" value="14"/>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
639 <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
640 </test>
20
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
641 <!-- Test that user-provided (variant-input option) sites are included in output -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
642 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
643 <param name="reference_source_selector" value="history" />
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
644 <param name="processmode" value="individual" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
645 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
646 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
20
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
647 <param name="options_type_selector" value="full"/>
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
648 <conditional name="optional_inputs">
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
649 <param name="optional_inputs_selector" value="set" />
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
650 <conditional name="input_variant_type">
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
651 <param name="input_variant_type_selector" value="provide_vcf" />
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
652 <param name="input_variant_vcf" value="freebayes-phix174-input-sites-test3.vcf.bgzip" />
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
653 </conditional>
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
654 </conditional>
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
655 <output name="output_vcf">
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
656 <assert_contents>
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
657 <has_line_matching expression="phiX174&#009;1134&#009;\.&#009;A&#009;\.&#009;.+"/>
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
658 </assert_contents>
ed8508ec9613 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cdd582adf568e80558740ec7ff51c9447948cf77
iuc
parents: 19
diff changeset
659 </output>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
660 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
661 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
662 <param name="reference_source_selector" value="history" />
8
b0ff6447545f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit d2f9b1728a6525b599e2c014a183b0415b27a870
iuc
parents: 7
diff changeset
663 <param name="processmode" value="individual" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
664 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
665 <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
666 <param name="options_type_selector" value="full"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
667 <param name="population_model_selector" value="set"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
668 <param name="P" value="1"/>
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
669 <param name="trim_complex_tail" value="--trim-complex-tail"/>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
670 <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
671 </test>
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
672 <test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
673 <param name="reference_source_selector" value="history" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
674 <param name="processmode" value="individual" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
675 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
676 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
677 <param name="options_type_selector" value="simple"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
678 <param name="coverage_options_selector" value="set" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
679 <param name="min_coverage" value="250" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
680 <output name="output_vcf" file="freebayes-hxb2-test5.vcf" lines_diff="4" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
681 </test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
682 <test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
683 <param name="reference_source_selector" value="history" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
684 <param name="processmode" value="individual" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
685 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
686 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
687 <param name="options_type_selector" value="simple"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
688 <param name="coverage_options_selector" value="set" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
689 <param name="limit_coverage" value="400" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
690 <output name="output_vcf" file="freebayes-hxb2-test6.vcf" lines_diff="4" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
691 </test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
692 <test>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
693 <param name="reference_source_selector" value="history" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
694 <param name="processmode" value="individual" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
695 <param name="ref_file" ftype="fasta" value="freebayes-hxb2.fasta"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
696 <param name="input_bams" ftype="bam" value="freebayes-hxb2.bam"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
697 <param name="options_type_selector" value="simple"/>
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
698 <param name="coverage_options_selector" value="set" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
699 <param name="skip_coverage" value="100" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
700 <output name="output_vcf" file="freebayes-hxb2-test7.vcf" lines_diff="4" />
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
701 </test>
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
702 <test> <!-- Test with CRAM -->
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
703 <param name="reference_source_selector" value="history" />
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
704 <param name="processmode" value="individual" />
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
705 <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
706 <param name="input_bams" ftype="cram" value="freebayes-phix174.cram"/>
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
707 <param name="options_type_selector" value="simple"/>
16
a2feedafda6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit be1c2e9e056710ef8b1110a121dc38c6e06dbbee"
iuc
parents: 15
diff changeset
708 <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="6" />
14
91271de440f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit cce7fcdd5e8ba8636c751f9f974bf07a6845ba1c"
iuc
parents: 13
diff changeset
709 </test>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
710 </tests>
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
711 <help><![CDATA[
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
712 **What it does**
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
713
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
714 FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
715
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
716 See https://github.com/ekg/freebayes for details on FreeBayes.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
717
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
718 ------
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
719
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
720 **Description**
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
721
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
722 Provided some BAM dataset(s) and a reference sequence, FreeBayes will produce a VCF dataset describing SNPs, indels, and complex variants in samples in the input alignments.
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
723
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
724 By default, FreeBayes will consider variants supported by at least 2 observations in a single sample (-C) and also by at least 20% of the reads from a single sample (-F). These settings are suitable to low to high depth sequencing in haploid and diploid samples, but users working with polyploid or pooled samples may wish to adjust them depending on the characteristics of their sequencing data.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
725
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
726 FreeBayes is capable of calling variant haplotypes shorter than a read length where multiple polymorphisms segregate on the same read. The maximum distance between polymorphisms phased in this way is determined by the --max-complex-gap, which defaults to 3bp. In practice, this can comfortably be set to half the read length.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
727
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
728 Ploidy may be set to any level (-p), but by default all samples are assumed to be diploid. FreeBayes can model per-sample and per-region variation in copy-number (-A) using a copy-number variation map.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
729
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
730 FreeBayes can act as a frequency-based pooled caller and describe variants and haplotypes in terms of observation frequency rather than called genotypes. To do so, use --pooled-continuous and set input filters to a suitable level. Allele observation counts will be described by AO and RO fields in the VCF output.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
731
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
732 -------
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
733
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
734 **Galaxy-specific options**
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
735
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
736 Galaxy allows five levels of control over FreeBayes options, provided by the **Choose parameter selection level** menu option. These are:
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
737
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
738 1. *Simple diploid calling*: The simplest possible FreeBayes application. Equivalent to using FreeBayes with only a BAM input and no other parameter options.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
739 2. *Simple diploid calling with filtering and coverage*: Same as #1 plus two additional options: -0 (standard filters: --min-mapping-quality 30 --min-base-quality 20 --min-supporting-allele-qsum 0 --genotype-variant-threshold 0) and --min-coverage.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
740 3. *Frequency-based pooled calling*: This is equivalent to using FreeBayes with the following options: --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --report-monomorphic. This is the best choice for calling variants in mixtures such as viral, bacterial, or organellar genomes.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
741 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
742 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy parameters.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
743
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
744 ------
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
745
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
746 **Command-line parameters**
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
747
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
748 **Input**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
749
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
750 --bam FILE The file or set of BAM files to be analyzed.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
751 --bam-list FILE A file containing a list of BAM files to be analyzed.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
752
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
753 --stdin Read BAM input on stdin.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
754 --fasta-reference FILE Use FILE as the reference sequence for analysis.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
755 An index file (FILE.fai) will be created if none exists.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
756 If neither --targets nor --region are specified, FreeBayes
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
757 will analyze every position in this reference.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
758 --targets FILE Limit analysis to targets listed in the BED-format FILE.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
759 --region <chrom>:<start>-<end> Limit analysis to the specified region, 0-base coordinates,
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
760 end_position not included (same as BED format).
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
761 Either '-' or '..' maybe used as a separator.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
762 --samples FILE Limit analysis to samples listed (one per line) in the FILE.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
763 By default FreeBayes will analyze all samples in its input
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
764 BAM files.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
765 --populations FILE Each line of FILE should list a sample and a population which
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
766 it is part of. The population-based bayesian inference model
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
767 will then be partitioned on the basis of the populations.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
768 --cnv-map FILE Read a copy number map from the BED file FILE, which has
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
769 either a sample-level ploidy:
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
770 sample_name copy_number
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
771 or a region-specific format:
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
772 seq_name start end sample_name copy_number
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
773 ... for each region in each sample which does not have the
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
774 default copy number as set by --ploidy. These fields can be delimited
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
775 by space or tab.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
776
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
777 **Output**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
778
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
779 --vcf FILE Output VCF-format results to FILE. (default: stdout)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
780 --gvcf Write gVCF output, which indicates coverage in uncalled regions.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
781 --gvcf-chunk NUM When writing gVCF output emit a record for every NUM bases.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
782 --gvcf-dont-use-chunk When writing the gVCF output emit a record for all bases if
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
783 set to "true" , will also route an int to --gvcf-chunk
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
784 similar to --output-mode EMIT_ALL_SITES from GATK
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
785 --variant-input VCF Use variants reported in VCF file as input to the algorithm.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
786 Variants in this file will included in the output even if
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
787 there is not enough support in the data to pass input filters.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
788 --only-use-input-alleles Only provide variant calls and genotype likelihoods for sites
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
789 and alleles which are provided in the VCF input, and provide
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
790 output in the VCF for all input alleles, not just those which
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
791 have support in the data.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
792 --haplotype-basis-alleles VCF When specified, only variant alleles provided in this input
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
793 VCF will be used for the construction of complex or haplotype
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
794 alleles.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
795 --report-all-haplotype-alleles At sites where genotypes are made over haplotype alleles,
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
796 provide information about all alleles in output, not only
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
797 those which are called.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
798 --report-monomorphic Report even loci which appear to be monomorphic, and report all
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
799 considered alleles, even those which are not in called genotypes.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
800 Loci which do not have any potential alternates have '.' for ALT.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
801 --pvar N Report sites if the probability that there is a polymorphism
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
802 at the site is greater than N. default: 0.0. Note that post-
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
803 filtering is generally recommended over the use of this parameter.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
804 --strict-vcf Generate strict VCF format (FORMAT/GQ will be an int)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
805
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
806 **Population model**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
807
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
808 --theta N The expected mutation rate or pairwise nucleotide diversity
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
809 among the population under analysis. This serves as the
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
810 single parameter to the Ewens Sampling Formula prior model
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
811 default: 0.001
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
812 --ploidy N Sets the default ploidy for the analysis to N. default: 2
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
813 --pooled-discrete Assume that samples result from pooled sequencing.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
814 Model pooled samples using discrete genotypes across pools.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
815 When using this flag, set --ploidy to the number of
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
816 alleles in each sample or use the --cnv-map to define
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
817 per-sample ploidy.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
818 --pooled-continuous Output all alleles which pass input filters, regardles of
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
819 genotyping outcome or model.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
820
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
821 **Reference allele**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
822
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
823 --use-reference-allele This flag includes the reference allele in the analysis as
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
824 if it is another sample from the same population.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
825 --reference-quality MQ,BQ Assign mapping quality of MQ to the reference allele at each
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
826 site and base quality of BQ. default: 100,60
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
827
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
828 **Allele scope**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
829
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
830 --use-best-n-alleles N Evaluate only the best N SNP alleles, ranked by sum of
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
831 supporting quality scores. (Set to 0 to use all; default: all)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
832 --max-complex-gap
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
833 --haplotype-length N Allow haplotype calls with contiguous embedded matches of up
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
834 to this length. Set N=-1 to disable clumping. (default: 3)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
835 --min-repeat-size When assembling observations across repeats, require the total repeat
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
836 length at least this many bp. (default: 5)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
837 --min-repeat-entropy N To detect interrupted repeats, build across sequence until it has
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
838 entropy > N bits per bp. Set to 0 to turn off. (default: 1)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
839 --no-partial-observations Exclude observations which do not fully span the dynamically-determined
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
840 detection window. (default, use all observations, dividing partial
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
841 support across matching haplotypes when generating haplotypes.)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
842
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
843 **Indel realignment**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
844
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
845 --dont-left-align-indels Turn off left-alignment of indels, which is enabled by default.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
846
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
847 **Input filters**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
848
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
849 --use-duplicate-reads Include duplicate-marked alignments in the analysis.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
850 default: exclude duplicates marked as such in alignments
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
851 --min-mapping-quality Q Exclude alignments from analysis if they have a mapping
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
852 quality less than Q. default: 1
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
853 --min-base-quality Q Exclude alleles from analysis if their supporting base
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
854 quality is less than Q. default: 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
855 --min-supporting-allele-qsum Q Consider any allele in which the sum of qualities of supporting
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
856 observations is at least Q. default: 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
857 --min-supporting-mapping-qsum Q Consider any allele in which and the sum of mapping qualities of
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
858 supporting reads is at least Q. default: 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
859 --mismatch-base-quality-threshold Q Count mismatches toward --read-mismatch-limit if the base
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
860 quality of the mismatch is >= Q. default: 10
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
861 --read-mismatch-limit N Exclude reads with more than N mismatches where each mismatch
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
862 has base quality >= mismatch-base-quality-threshold.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
863 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
864 --read-max-mismatch-fraction N Exclude reads with more than N [0,1] fraction of mismatches where
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
865 each mismatch has base quality >= mismatch-base-quality-threshold
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
866 default: 1.0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
867 --read-snp-limit N Exclude reads with more than N base mismatches, ignoring gaps
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
868 with quality >= mismatch-base-quality-threshold.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
869 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
870 --read-indel-limit N Exclude reads with more than N separate gaps.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
871 default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
872 --standard-filters Use stringent input base and mapping quality filters
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
873 Equivalent to -m 30 -q 20 -R 0 -S 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
874 --min-alternate-fraction N Require at least this fraction of observations supporting
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
875 an alternate allele within a single individual in the
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
876 in order to evaluate the position. default: 0.05
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
877 --min-alternate-count N Require at least this count of observations supporting
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
878 an alternate allele within a single individual in order
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
879 to evaluate the position. default: 2
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
880 --min-alternate-qsum N Require at least this sum of quality of observations supporting
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
881 an alternate allele within a single individual in order
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
882 to evaluate the position. default: 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
883 --min-alternate-total N Require at least this count of observations supporting
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
884 an alternate allele within the total population in order
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
885 to use the allele in analysis. default: 1
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
886 --min-coverage N Require at least this coverage to process a site. default: 0
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
887 --limit-coverage N Downsample per-sample coverage to this level if greater than this coverage.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
888 default: no limit
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
889 --skip-coverage N Skip processing of alignments overlapping positions with coverage >N.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
890 This filters sites above this coverage, but will also reduce data nearby.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
891 default: no limit
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
892
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
893 **Population priors**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
894
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
895 --no-population-priors Equivalent to --pooled-discrete --hwe-priors-off and removal of
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
896 Ewens Sampling Formula component of priors.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
897
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
898 **Mappability priors**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
899
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
900 --hwe-priors-off Disable estimation of the probability of the combination
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
901 arising under HWE given the allele frequency as estimated
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
902 by observation frequency.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
903 --binomial-obs-priors-off Disable incorporation of prior expectations about observations.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
904 Uses read placement probability, strand balance probability,
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
905 and read position (5'-3') probability.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
906 --allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
907 as a component of the priors.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
908
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
909 **Genotype likelihoods**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
910
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
911 --observation-bias FILE Read length-dependent allele observation biases from FILE.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
912 The format is [length] [alignment efficiency relative to reference]
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
913 where the efficiency is 1 if there is no relative observation bias.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
914 --base-quality-cap Q Limit estimated observation quality by capping base quality at Q.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
915 --prob-contamination F An estimate of contamination to use for all samples. default: 10e-9
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
916 --legacy-gls Use legacy (polybayes equivalent) genotype likelihood calculations
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
917 --contamination-estimates FILE A file containing per-sample estimates of contamination, such as
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
918 those generated by VerifyBamID. The format should be:
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
919 sample p(read=R|genotype=AR) p(read=A|genotype=AA)
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
920 Sample '*' can be used to set default contamination estimates.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
921
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
922 **Algorithmic features**::
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
923
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
924 --report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
925 from genotype likelihoods.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
926 --genotyping-max-iterations N Iterate no more than N times during genotyping step. default: 1000.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
927 --genotyping-max-banddepth N Integrate no deeper than the Nth best genotype by likelihood when
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
928 genotyping. default: 6.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
929 --posterior-integration-limits N,M Integrate all genotype combinations in our posterior space
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
930 which include no more than N samples with their Mth best
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
931 data likelihood. default: 1,3.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
932 --exclude-unobserved-genotypes Skip sample genotypings for which the sample has no supporting reads.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
933 --genotype-variant-threshold N Limit posterior integration to samples where the second-best
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
934 genotype likelihood is no more than log(N) from the highest
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
935 genotype likelihood for the sample. default: ~unbounded
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
936 --use-mapping-quality Use mapping quality of alleles when calculating data likelihoods.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
937 --harmonic-indel-quality Use a weighted sum of base qualities around an indel, scaled by the
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
938 distance from the indel. By default use a minimum BQ in flanking sequence.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
939 --read-dependence-factor N Incorporate non-independence of reads by scaling successive
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
940 observations by this factor during data likelihood
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
941 calculations. default: 0.9
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
942 --genotype-qualities Calculate the marginal probability of genotypes and report as GQ in
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
943 each sample field in the VCF output.
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
944
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
945 ------
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
946
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
947 **Acknowledgments**
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
948
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
949 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
9
c07ad8a9c701 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
iuc
parents: 8
diff changeset
950 TNG was developed by Bjoern Gruening.
11
f14331392369 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 24f33bda62a7b6771ad42a39fe8c683e09f6d8b8"
iuc
parents: 10
diff changeset
951 ]]>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
952 </help>
10
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
953 <expand macro="citations">
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
954 <citation type="bibtex">
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
955 @article{Tange2011a,
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
956 title = {GNU Parallel - The Command-Line Power Tool},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
957 author = {O. Tange},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
958 address = {Frederiksberg, Denmark},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
959 journal = {;login: The USENIX Magazine},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
960 month = {Feb},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
961 number = {1},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
962 volume = {36},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
963 url = {http://www.gnu.org/s/parallel},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
964 year = {2011},
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
965 pages = {42-47}
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
966 }
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
967 </citation>
2fb16f415220 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b
iuc
parents: 9
diff changeset
968 </expand>
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
969 </tool>