Mercurial > repos > devteam > freebayes

annotate freebayes.xml @ 6:3aacf7637e02 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:40:47 -0500
parents 0f44dd2e7fe3
children d0997bd93c49
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
1 <tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-2">
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>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
3 <macros>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
4 <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
5 </macros>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
6 <requirements>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
7 <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
8 <requirement type="package" version="0.1.19">samtools</requirement>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
9 <requirement type="package" version="4.1.3">gawk</requirement>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
10 <requirement type="package" version="20160622">parallel</requirement>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
11 </requirements>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
12 <stdio>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
13 <exit_code range="1:" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
14 </stdio>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
15 <command><![CDATA[
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
16 ##set up input files
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
17
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
18 #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
19
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
20 #if str( $reference_source.reference_source_selector ) == "history":
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
21 ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
22 samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 &&
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
23 #else:
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
24 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
25 #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
26
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
27 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
28 ln -s -f '${input_bam}' 'b_${bam_count}.bam' &&
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
29 ln -s -f '${input_bam.metadata.bam_index}' 'b_${bam_count}.bam.bai' &&
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
30 #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
31
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
32 ## Tabixize optional input_variant_vcf file (for --variant-input option)
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
33 #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( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
34 ln -s -f '${options_type.optional_inputs.input_variant_type.input_variant_vcf}' 'input_variant_vcf.vcf.gz' &&
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
35 ln -s -f '${Tabixized_input}' 'input_variant_vcf.vcf.gz.tbi' &&
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
36 #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
37
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
38 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
39 samtools view -H b_${bam_count}.bam |
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
40 grep "^@SQ" |
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
41 cut -f 2- |
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
42 awk '{ gsub("^SN:","",$1);
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
43 gsub("^LN:","",$2);
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
44 print $1"\t0\t"$2; }' >> regions_all.bed &&
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
45 #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
46
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
47 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
48 ## 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
49 ## 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
50
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
51 mkdir vcf_output &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
52 mkdir failed_alleles &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
53 mkdir trace &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
54
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
55 ## 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
56
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
57 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
58 do
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
59
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
60 echo "
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
61
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
62 ## 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
63
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
64 freebayes
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
65
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
66 --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
67
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
68 #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
69 --bam 'b_${bam_count}.bam'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
70 #end for
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
71 --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
72
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
73 ## Outputs
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
74 --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
75
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
76 #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
77 --targets '${target_limit_type.input_target_bed}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
78 #elif str( $target_limit_type.target_limit_type_selector ) == "limit_by_region":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
79 --region '${target_limit_type.region_chromosome}:${target_limit_type.region_start}..${target_limit_type.region_end}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
80 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
81
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
82 ##advanced options
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
83 #if str( $options_type.options_type_selector ) == "simple":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
84 ##do nothing as command like build up to this point is sufficinet for simple diploid calling
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 #elif str( $options_type.options_type_selector ) == "simple_w_filters":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
87 --standard-filters
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
88 --min-coverage '${options_type.min_coverage}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
89 #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
90 --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
91 --min-alternate-count 1
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
92 --min-alternate-fraction 0
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
93 --pooled-continuous
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
94 --report-monomorphic
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
95 #elif str( $options_type.options_type_selector ) == "naive_w_filters":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
96 --haplotype-length 0
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
97 --min-alternate-count 1
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
98 --min-alternate-fraction 0
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
99 --pooled-continuous
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
100 --report-monomorphic
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
101 --standard-filters
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
102 --min-coverage '${options_type.min_coverage}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
103
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
104 ## Command line direct text entry is not allowed at this time for security reasons
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 ) == "full":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
106 #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
107 ${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
108
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
109 #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
110 --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
111 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
112 #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
113 --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
114 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
115 #if $options_type.optional_inputs.samples:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
116 --samples '${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
117 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
118 #if $options_type.optional_inputs.populations:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
119 --populations '${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
120 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
121 #if $options_type.optional_inputs.A:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
122 --cnv-map '${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
123 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
124 #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
125 --variant-input 'input_variant_vcf.vcf.gz' ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_variant_vcf file" section of the command line above
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
126 ${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
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 $options_type.optional_inputs.haplotype_basis_alleles:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
129 --haplotype-basis-alleles '${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
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 $options_type.optional_inputs.observation_bias:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
132 --observation-bias '${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
133 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
134 #if $options_type.optional_inputs.contamination_estimates:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
135 --contamination-estimates '${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
136 #end if
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
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
138
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
139 ## REPORTING
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
140 #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
141 --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
142 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
143 ## POPULATION MODEL
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
144 #if str( $options_type.population_model.population_model_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
145 --theta '${options_type.population_model.T}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
146 --ploidy '${options_type.population_model.P}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
147 ${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
148 ${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
149 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
150
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
151 ## REFERENCE ALLELE
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.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
153 ${options_type.reference_allele.Z}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
154 --reference-quality '${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
155 #end if
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
156
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
157 ## ALLELE SCOPE
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
158 #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
159 ${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
160 ${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
161 ${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
162 ${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
163 ${options_type.allele_scope.no_partial_observations}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
164
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
165 -n '${options_type.allele_scope.n}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
166
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
167 --haplotype-length '${options_type.allele_scope.haplotype_length}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
168 --min-repeat-size '${options_type.allele_scope.min_repeat_length}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
169 --min-repeat-entropy '${options_type.allele_scope.min_repeat_entropy}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
170 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
171
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
172 ## REALIGNMENT
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
173 ${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
174
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
175 ##INPUT FILTERS
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
176 #if str( $options_type.input_filters.input_filters_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
177 ${options_type.input_filters.use_duplicate_reads}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
178 -m '${options_type.input_filters.m}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
179 -q '${options_type.input_filters.q}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
180 -R '${options_type.input_filters.R}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
181 -Y '${options_type.input_filters.Y}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
182 -e '${options_type.input_filters.e}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
183 -F '${options_type.input_filters.F}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
184 -C '${options_type.input_filters.C}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
185 -G '${options_type.input_filters.G}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
186
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
187 #if str( $options_type.input_filters.mismatch_filters.mismatch_filters_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
188 -Q '${options_type.input_filters.mismatch_filters.Q}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
189 -U '${options_type.input_filters.mismatch_filters.U}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
190 -z '${options_type.input_filters.mismatch_filters.z}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
191
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
192 --read-snp-limit '${options_type.input_filters.mismatch_filters.read_snp_limit}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
193 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
194
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
195 --min-coverage '${options_type.input_filters.min_coverage}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
196 --min-alternate-qsum "${options_type.input_filters.min_alternate_qsum}"
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
197 #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
198
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
199 ## 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
200 #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
201 ${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
202 ${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
203 ${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
204 ${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
205 #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
206
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
207 ## GENOTYPE LIKELIHOODS
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
208 #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
209 ${$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
210
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
211 --base-quality-cap '${$options_type.genotype_likelihoods.base_quality_cap}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
212 --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
213 #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
214
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
215 ## ALGORITHMIC FEATURES
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
216 #if str( $options_type.algorithmic_features.algorithmic_features_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
217 -B '${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
218 -W '${options_type.algorithmic_features.W}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
219 -D '${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
220
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
221 #if str( $options_type.algorithmic_features.genotype_variant_threshold.genotype_variant_threshold_selector ) == "set":
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
222 -S '${options_type.algorithmic_features.genotype_variant_threshold.S}'
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
223 #end if
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
224
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
225 ${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
226 ${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
227 ${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
228 ${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
229 ${options_type.algorithmic_features.report_genotype_likelihood_max}
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
230
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
231 --genotyping-max-banddepth '${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
232 #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
233 #end if
9f3d6c3098ac planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents: 2
diff changeset
234
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
235 ";
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
236 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
237
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
238 cat freebayes_commands.sh |
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
239 parallel --no-notice -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
240
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
241 ## 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
242 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
243
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
244 for i in `cat regions_uniq.bed | awk '{print $1":"$2".."$3}'`;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
245 do
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
246 ## if this fails then it bails out the script
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
247 cat "./vcf_output/part_\$i.vcf" | grep -v "^#" || true
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
248 ;
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
249 done | sort -k1,1 -k2,2n -k5,5 -u | cat header.txt - > '${output_vcf}'
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
250
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
251 #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
252 #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
253 #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
254 &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
255 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
256 do
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
257 cat "./failed_alleles/part_\$i.bed"
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
258 ;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
259 done > '${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
260 #end if
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
261
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
262 #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
263 &&
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
264 for i in `cat regions.bed | awk '{print $1":"$2".."$3}'`;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
265 do
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
266 cat './trace/part_\$i.txt'
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
267 ;
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
268 done > '${output_trace}'
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
269 #end if
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
270 #end if
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
271 #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
272 ]]></command>
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
273
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
274 <inputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
275 <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
276 <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
277 <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
278 <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
279 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
280 <when value="cached">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
281 <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
282 <validator type="unspecified_build" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
283 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
284 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
285 <param name="ref_file" type="select" label="Using reference genome">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
286 <options from_data_table="fasta_indexes"></options>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
287 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
288 </param>
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
289 </when>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
290 <when value="history"> <!-- FIX ME!!!! -->
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="input_bams" type="data" format="bam" multiple="True" label="BAM file" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
292 <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
293 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
294 </when>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
295 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
296 <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
297 <param name="target_limit_type_selector" type="select" label="Limit variant calling to a set of regions?" help="Sets --targets or --region options">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
298 <option value="do_not_limit" selected="True">Do not limit</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
299 <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
300 <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
301 </param>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
302 <when value="do_not_limit" /><!-- Do nothing here -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
303 <when value="limit_by_target_file">
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
304 <param name="input_target_bed" type="data" format="bed" label="Limit analysis to regions in a file (BED-format)." argument="--targets"/>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
305 </when>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
306 <when value="limit_by_region">
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
307 <param name="region_chromosome" type="text" label="Region Chromosome" value="" argument="--region"/> <!--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
308 <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
309 <param name="region_end" type="integer" label="Region End" value="" />
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
310 </when>
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
311 </conditional>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
312 <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
313 <param name="options_type_selector" type="select" label="Choose parameter selection level"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
314 help="Select how much control over the freebayes run you need" >
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
315 <option value="simple" selected="True">1. Simple diploid calling</option>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
316 <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
317 <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
318 <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
319 <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
320 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
321 <when value="full">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
322 <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
323 <param name="optional_inputs_selector" type="select" label="Additional inputs"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
324 help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --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
325 --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
326 <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
327 <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
328 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
329 <when value="set">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
330 <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" 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
331 label="Write out failed alleles file" argument="--failed-alleles" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
332 <param name="output_trace_option" type="boolean" truevalue="--trace" 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
333 label="Write out algorithm trace file" argument="--trace"/>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
334 <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
335 help="default=By default FreeBayes will analyze all samples in its input BAM files" argument="--samples"/>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
336 <param name="populations" type="data" format="txt" label="Populations File" optional="True"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
337 help="Each line of FILE should list a sample and a population which it is part of. The population-based bayesian inference model will
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
338 then be partitioned on the basis of the populations. [default=False]"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
339 argument="--populations" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
340 <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
341 help="default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format:
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
342 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."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
343 argument="--cnv-map" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
344 <conditional name="input_variant_type">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
345 <param name="input_variant_type_selector" type="select" label="Provide variants file">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
346 <option value="do_not_provide" selected="True">Do not provide</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
347 <option value="provide_vcf">Provide VCF file</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
348 </param>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
349 <when value="do_not_provide" /><!-- Do nothing here -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
350 <when value="provide_vcf">
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
351 <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm" argument="--variant-input">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
352 <conversion name="Tabixized_input" type="tabix" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
353 </param>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
354 <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
355 label="Only provide variant calls and genotype likelihoods for sites in VCF" argument="--only-use-input-alleles" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
356 </when>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
357 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
358 <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
359 argument="--haplotype-basis-alleles" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
360 <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" 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
361 label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
362 argument="--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
363 <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
364 help="The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
365 argument="--observation-bias" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
366 <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
367 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."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
368 argument="--contamination-estimates" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
369 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
370 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
371 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
372
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
373 <!-- reporting -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
374 <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
375 <param name="reporting_selector" type="select" label="Reporting options" help="Sets -P --pvar option">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
376 <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
377 <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
378 </param>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
379 <when value="set">
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
380 <param name="pvar" type="float" value="0.0" label="Report sites if the probability that there is a polymorphism at the site is greater than"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
381 help="Note that post-filtering is generally recommended over the use of this parameter. [default=0.0]"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
382 argument="--pvar" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
383 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
384 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
385 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
386
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
387 <!-- population model -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
388 <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
389 <param name="population_model_selector" type="select" label="Population model options"
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
390 help="Sets --theta, --ploidy, --pooled-discrete, and --pooled-continuous options " >
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
391 <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
392 <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
393 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
394 <when value="set">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
395 <param name="T" type="float" value="0.001" label="The expected mutation rate or pairwise nucleotide diversity among the population under analysis"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
396 help="This serves as the single parameter to the Ewens Sampling Formula prior model. [default = 0.001]" argument='--theta'/>
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
397 <param name="P" type="integer" value="2" label="Set ploidy for the analysis"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
398 help="default=2" argument='--ploidy' />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
399 <param name="J" type="boolean" truevalue="-J" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
400 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. [default=False]"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
401 argument="--pooled-discrete"/>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
402 <param name="K" type="boolean" truevalue="-K" falsevalue="" checked="False" label="Output all alleles which pass input filters, regardles of genotyping outcome or model"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
403 help="default=False." argument="--poled-continuous" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
404 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
405 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
406 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
407
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
408 <!-- reference allele -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
409 <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
410 <param name="reference_allele_selector" type="select" label="Reference allele options"
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
411 help="Sets --use-reference-allele and --reference-quality options.">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
412 <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
413 <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
414 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
415 <when value="set">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
416 <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
417 help="default=False" argument="--use-reference-allele" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
418 <param name="reference_quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
419 help="default=100,60" argument="--reference-quality" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
420 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
421 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
422 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
423
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
424 <!-- allelic scope -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
425 <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
426 <param name="allele_scope_selector" type="select" label="Allelic scope options"
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
427 help="Sets -I, i, -X, -u, -n, --haplotype-length, --min-repeat-size, --min-repeat-entropy, and --no-partial-observations options.">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
428 <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
429 <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
430 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
431 <when value="set">
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
432 <param name="I" type="boolean" truevalue="-I" falsevalue="" checked="False" label="Ignore SNP alleles"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
433 help="default=False" argument="--no-snps" />
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
434 <param name="i" type="boolean" truevalue="-i" falsevalue="" checked="False" label="Ignore indels alleles"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
435 help="default=False" argument="--no-indels" />
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
436 <param name="X" type="boolean" truevalue="-X" falsevalue="" checked="False" label="Ignore multi-nucleotide polymorphisms, MNPs"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
437 help="default=False" argument="--no-mnps" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
438 <param name="u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)."
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
439 help="default=False" argument="--no-complex" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
440 <param name="n" type="integer" value="0" label="How many best SNP alleles to evaluate"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
441 help="Alleles are ranked by the sum of supporting quality scores. Set to 0 to evaluate all. [default=0 (all)]"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
442 argument="--use-best-n-alleles" />
4
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="haplotype_length" type="integer" value="3" label="Allow haplotype calls with contiguous embedded matches of up to (nucleotides)"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
444 help="-E --max-complex-gap --haplotype-length; default=3." />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
445 <param name="min_repeat_length" type="integer" value="5" label="When assembling observations across repeats, require the total repeat length at least this many bp"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
446 help="default=5." argument="--min-repeat-size" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
447 <param name="min_repeat_entropy" type="integer" value="0" label="To detect interrupted repeats, build across sequence until it has entropy > (bits per bp)"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
448 help="default=0 (off)." argument="--min-repeat-entropy" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
449 <param name="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
450 label="Exclude observations which do not fully span the dynamically-determined detection window"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
451 help="default=use all observations, dividing partial support across matching haplotypes when generating haplotypes."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
452 argument="--no-partial-observations" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
453 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
454 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
455 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
456
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
457 <!-- indel realignment -->
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
458 <param name="O" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Turn off left-alignment of indels"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
459 help="default=False (do left align)." argument="--dont-left-align-indels" />
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
460
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
461 <!-- input filters -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
462 <conditional name="input_filters">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
463 <param name="input_filters_selector" type="select" label="Input filters"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
464 help="Sets -4, -m, -q, -R, -Y, -Q, -U, -z, -&#36;, -e, -0, -F, -C, -3, -G, and -&#33; options.">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
465 <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
466 <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
467 </param>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
468 <when 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
469 <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" 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
470 label="Include duplicate-marked alignments in the analysis."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
471 help="default=False (exclude duplicates marked as such in alignments)." argument="--use-duplicate-reads" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
472 <param name="m" type="integer" value="1" label="Exclude alignments from analysis if they have a mapping quality less than"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
473 help="default=1" argument="--min-mapping-quality" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
474 <param name="q" type="integer" value="0" label="Exclude alleles from analysis if their supporting base quality less than"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
475 help="default=0" argument="--min-base-quality" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
476 <param name="R" type="integer" value="0" label="Consider any allele in which the sum of qualities of supporting observations is at least"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
477 help="default=0" argument="--min-supporting-allele-qsum" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
478 <param name="Y" type="integer" value="0" label="Consider any allele in which and the sum of mapping qualities of supporting reads is at least"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
479 help="default=0" argument="--min-supporting-mapping-qsum" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
480 <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
481 <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
482 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
483 <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
484 <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
485 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
486 <when value="set">
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
487 <param name="Q" type="integer" value="10"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
488 label="Count mismatches toward -U (option below) if the base quality of the mismatch is >="
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
489 help="default=10" argument="--mismatch-base-quality-threshold" />
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
490 <param name="U" type="integer" value="1000" optional="True"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
491 label="Exclude reads with more than N mismatches where each mismatch has base quality >= Q (option above)"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
492 help="default=~unbound" argument="--read-mismatch-limit" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
493 <param name="z" type="float" value="1.0" min="0.0" max="1.0"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
494 label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= Q (second option above)"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
495 help="default=1.0" argument="--read-max-mismatch-fraction" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
496 <param name="read_snp_limit" type="integer"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
497 value="1000" label="Exclude reads with more than N base mismatches, ignoring gaps with quality >= Q (third option abobe)"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
498 argument="--read-snp-limit" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
499 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
500 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
501 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
502 <param name="e" type="integer" value="1000" label="Exclude reads with more than this number of separate gaps"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
503 help="default=~unbounded" argument="--read-snp-limit" />
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
504 <param name="standard_filters" type="boolean" truevalue="-0" falsevalue="" checked="False"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
505 label="Use stringent input base and mapping quality filters"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
506 help="default=False. Equivalent to -m 30 -q 20 -R 0 -S 0" argument="--standard-filters"/>
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
507 <param name="F" type="float" value="0.2"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
508 label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
509 help="default=0.2" argument="--min-alternate-fraction" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
510 <param name="C" type="integer" value="2"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
511 label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
512 help="default=2" argument="--min-alternate-count" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
513 <param name="min_alternate_qsum" type="integer" value="0"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
514 label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
515 help="default=0" argument="--min-alternate-qsum" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
516 <param name="G" type="integer" value="1"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
517 label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
518 help="default=1" argument="--min-alternate-total" />
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
519 <expand macro="par_min_cov" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
520 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
521 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
522 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
523
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
524 <!-- 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
525 <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
526 <param name="population_mappability_priors_selector" type="select" label="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
527 help="Sets -k, -w, -V, and -a options.">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
528 <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
529 <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
530 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
531 <when value="set">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
532 <param name="k" type="boolean" truevalue="-k" falsevalue="" checked="False" label="No population priors"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
533 help="default=False. Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
534 argument="--no-population-priors" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
535 <param name="w" type="boolean" truevalue="-w" 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
536 label="Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
537 help="default=False" argument="--hwe-priors-off" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
538 <param name="V" type="boolean" truevalue="-V" falsevalue="" checked="False" label="Disable incorporation of prior expectations about observations"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
539 help="default=False. Uses read placement probability, strand balance probability, and read position (5&#39;'-3&#39;') probability."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
540 argument="--binomial-obs-priors-off" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
541 <param name="a" type="boolean" truevalue="-a" 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
542 label="Disable use of aggregate probability of observation balance between alleles as a component of the priors"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
543 help="default=False"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
544 argument="--allele-balance-priors-off" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
545 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
546 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
547 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
548
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
549 <!-- genotype likelihoods -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
550 <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
551 <param name="genotype_likelihoods_selector" type="select" label="Genotype likelihood options"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
552 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
553 <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
554 <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
555 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
556 <when value="set">
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
557 <param name="base_quality_cap" type="integer" value="0" label="Limit estimated observation quality by capping base quality at"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
558 argument="--base-quality-cap" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
559 <param name="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
560 label="Generate genotype likelihoods using 'effective base depth' metric qual = 1-BaseQual * 1-MapQual"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
561 help="Incorporate partial observations. This is the default when contamination estimates are provided. Optimized for diploid samples."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
562 argument="--experimental-gls" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
563 <param name="prob_contamination" type="float" value="10e-9" label="An estimate of contamination to use for all samples"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
564 help="default=10e-9." argument="--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
565 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
566 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
567 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
568
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
569 <!-- algorithmic features -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
570 <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
571 <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
572 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
573 <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
574 <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
575 </param>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
576 <when value="set">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
577 <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" 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
578 label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
579 help="default=False" argument="--report-genotype-likelihood-max" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
580 <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
581 help="default=1000." argument="--genotyping-max-iterations" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
582 <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
583 help="default=6" argument="--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
584 <param name="W" type="text" value="1,3"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
585 label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
586 help="default=1,3" argument="--posterior-integration-limits" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
587 <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" 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
588 label="Skip sample genotypings for which the sample has no supporting reads"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
589 help="default=False" argument="--exclude-unobserved-genotypes" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
590 <conditional name="genotype_variant_threshold">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
591 <param name="genotype_variant_threshold_selector" type="select"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
592 label="Limit posterior integration" argument="--genotype-variant-threshold">
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
593 <option value="do_not_set" selected="true">Do not limit posterior integration</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
594 <option value="set">Set posterior integration limit</option>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
595 </param>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
596 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
597 <when value="set">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
598 <param name="S" value="" type="integer"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
599 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."
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
600 help="default=~unbounded" argument="--genotype-variant-threshold" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
601 </when>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
602 </conditional>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
603 <param name="j" type="boolean" truevalue="-j" falsevalue="" checked="False"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
604 label="Use mapping quality of alleles when calculating data likelihoods"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
605 help="default=False" argument="--use-mapping-quality" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
606 <param name="H" 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
607 label="Use a weighted sum of base qualities around an indel, scaled by the distance from the indel"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
608 help="default=use a minimum Base Quality in flanking sequence." argument="--harmonic-indel-quality" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
609 <param name="D" type="float" value="0.9" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations"
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
610 help="default=0.9." argument="--read-dependence-factor" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
611 <param name="genotype_qualities" type="boolean" truevalue="--genotype-qualities" 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
612 label="Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output"
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
613 help="-= --genotype-qualities; default=False " />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
614 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
615 <when value="do_not_set" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
616 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
617 </when>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
618 <when value="simple" /><!-- do nothing -->
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
619 <when value="simple_w_filters">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
620 <!-- add standard-filters to command line -->
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
621 <expand macro="par_min_cov" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
622 </when>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
623 <when value="naive">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
624 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic -->
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
625 </when>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
626 <when value="naive_w_filters">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
627 <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic 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
628 <expand macro="par_min_cov" />
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
629 </when>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
630 </conditional>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
631 </inputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
632 <outputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
633 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
634 <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
635 <filter>( options_type['options_type_selector'] == 'cline' or options_type['options_type_selector'] == 'full' ) and options_type['optional_inputs']['optional_inputs_selector'] == 'set' and options_type['optional_inputs']['output_failed_alleles_option'] is True</filter>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
636 </data>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
637 <data format="txt" name="output_trace" label="${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
638 <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
639 </data>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
640 </outputs>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
641 <tests>
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" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
644 <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
645 <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
646 <param name="options_type_selector" value="simple"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
647 <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
648 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
649 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
650 <param name="reference_source_selector" value="history" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
651 <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
652 <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
653 <param name="options_type_selector" value="naive_w_filters"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
654 <param name="min_coverage" value="14"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
655 <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
656 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
657 <test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
658 <param name="reference_source_selector" value="history" />
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
659 <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
660 <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
661 <param name="options_type_selector" value="naive_w_filters"/>
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="min_coverage" value="14"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
663 <output name="output_vcf" file="freebayes-phix174-test3.vcf" compare="contains"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
664 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
665 <test>
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="reference_source_selector" value="history" />
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="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
668 <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
669 <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
670 <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
671 <param name="P" value="1"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
672 <output name="output_vcf" file="freebayes-phix174-test4.vcf" compare="contains"/>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
673 </test>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
674 </tests>
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
675 <help>
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
676 **What it does**
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
677
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
678 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
679
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
680 See https://github.com/ekg/freebayes for details on FreeBayes.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
681
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
682 ------
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
683
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
684 **Description**
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
685
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
686 Privided BAM file(s) and a reference. FreeBayes will provide VCF output on standard out describing SNPs, indels, and complex variants in samples in the input alignments.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
687
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
688 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
689
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
690 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
691
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
692 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
693
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
694 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
695
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
696 -------
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
697
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
698 **Galaxy-specific options**
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
699
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
700 Galaxy allows five levels of control over FreeBayes options provided by **Choose parameter selection level** menu option. These are:
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
701
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
702 1. *Simple diploid calling*: The simples possible FreeBayes application. Equvalent of using FreeBayes with only a BAM input and no other parameter options.
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
703 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-varinat-threshold 0) and --min-coverage.
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
704 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 varinats in mixtures such as viral, bacterial, or organellar genomes.
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
705 4. *Frequency-based pooled calling with filtering and coverage*: Same as #3 but adds -0 and --min-coverage like in #2.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
706 5. *Complete list of all options*: Gives you full control by exposing all FreeBayes options as Galaxy widgets.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
707
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
708 -----
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
709
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
710 **FreeBayes options**
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
711
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
712 .. class:: infomark
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
713
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
714 Note that each Galaxy parameter widget corresponding to command line flags listed below:
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
715
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
716 Input and output::
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
717
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
718 -t --targets FILE
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
719 Limit analysis to targets listed in the BED-format FILE.
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
720 -r --region chrom:start_position-end_position
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
721 Limit analysis to the specified region, 0-base coordinates,
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
722 end_position included. Either '-' or '..' maybe used as a separator.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
723 -s --samples FILE
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
724 Limit analysis to samples listed (one per line) in the FILE.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
725 By default FreeBayes will analyze all samples in its input
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
726 BAM files.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
727 --populations FILE
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
728 Each line of FILE should list a sample and a population which
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
729 it is part of. The population-based bayesian inference model
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
730 will then be partitioned on the basis of the populations.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
731 -A --cnv-map FILE
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
732 Read a copy number map from the BED file FILE, which has
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
733 the format:
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
734 reference sequence, start, end, sample name, copy number
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
735 ... for each region in each sample which does not have the
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
736 default copy number as set by --ploidy.
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
737 --trace FILE Output an algorithmic trace to FILE.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
738 --failed-alleles FILE
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
739 Write a BED file of the analyzed positions which do not
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
740 pass --pvar to FILE.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
741 -@ --variant-input VCF
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
742 Use variants reported in VCF file as input to the algorithm.
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
743 Variants in this file will be treated as putative variants
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
744 even if there is not enough support in the data to pass
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
745 input filters.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
746 -l --only-use-input-alleles
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
747 Only provide variant calls and genotype likelihoods for sites
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
748 and alleles which are provided in the VCF input, and provide
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
749 output in the VCF for all input alleles, not just those which
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
750 have support in the data.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
751 --haplotype-basis-alleles VCF
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
752 When specified, only variant alleles provided in this input
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
753 VCF will be used for the construction of complex or haplotype
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
754 alleles.
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
755 --report-all-haplotype-alleles
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
756 At sites where genotypes are made over haplotype alleles,
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
757 provide information about all alleles in output, not only
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
758 those which are called.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
759 --report-monomorphic
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
760 Report even loci which appear to be monomorphic, and report all
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
761 considered alleles, even those which are not in called genotypes.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
762 Loci which do not have any potential alternates have '.' for ALT.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
763
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
764 Reporting::
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
765
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
766 -P --pvar N Report sites if the probability that there is a polymorphism
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
767 at the site is greater than N. default: 0.0. Note that post-
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
768 filtering is generally recommended over the use of this parameter.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
769
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
770 Population model::
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
771
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
772 -T --theta N The expected mutation rate or pairwise nucleotide diversity
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
773 among the population under analysis. This serves as the
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
774 single parameter to the Ewens Sampling Formula prior model
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
775 default: 0.001
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
776 -p --ploidy N Sets the default ploidy for the analysis to N. default: 2
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
777 -J --pooled-discrete
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
778 Assume that samples result from pooled sequencing.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
779 Model pooled samples using discrete genotypes across pools.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
780 When using this flag, set --ploidy to the number of
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
781 alleles in each sample or use the --cnv-map to define
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
782 per-sample ploidy.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
783 -K --pooled-continuous
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
784 Output all alleles which pass input filters, regardles of
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
785 genotyping outcome or model.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
786
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
787 Reference allele::
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
788
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
789 -Z --use-reference-allele
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
790 This flag includes the reference allele in the analysis as
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
791 if it is another sample from the same population.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
792 --reference-quality MQ,BQ
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
793 Assign mapping quality of MQ to the reference allele at each
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
794 site and base quality of BQ. default: 100,60
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
795
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
796 Allele scope::
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
797
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
798 -I --no-snps Ignore SNP alleles.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
799 -i --no-indels Ignore insertion and deletion alleles.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
800 -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
801 -u --no-complex Ignore complex events (composites of other classes).
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
802 -n --use-best-n-alleles N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
803 Evaluate only the best N SNP alleles, ranked by sum of
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
804 supporting quality scores. (Set to 0 to use all; default: all)
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
805 -E --max-complex-gap N
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
806 --haplotype-length N
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
807 Allow haplotype calls with contiguous embedded matches of up
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
808 to this length. (default: 3)
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
809 --min-repeat-size N
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
810 When assembling observations across repeats, require the total repeat
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
811 length at least this many bp. (default: 5)
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
812 --min-repeat-entropy N
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
813 To detect interrupted repeats, build across sequence until it has
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
814 entropy > N bits per bp. (default: 0, off)
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
815 --no-partial-observations
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
816 Exclude observations which do not fully span the dynamically-determined
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
817 detection window. (default, use all observations, dividing partial
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
818 support across matching haplotypes when generating haplotypes.)
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
819
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
820 Indel realignment::
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
821
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
822 -O --dont-left-align-indels
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
823 Turn off left-alignment of indels, which is enabled by default.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
824
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
825 Input filters::
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
826
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
827 -4 --use-duplicate-reads
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
828 Include duplicate-marked alignments in the analysis.
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
829 default: exclude duplicates marked as such in alignments
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
830 -m --min-mapping-quality Q
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
831 Exclude alignments from analysis if they have a mapping
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
832 quality less than Q. default: 1
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
833 -q --min-base-quality Q
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
834 Exclude alleles from analysis if their supporting base
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
835 quality is less than Q. default: 0
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
836 -R --min-supporting-allele-qsum Q
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
837 Consider any allele in which the sum of qualities of supporting
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
838 observations is at least Q. default: 0
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
839 -Y --min-supporting-mapping-qsum Q
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
840 Consider any allele in which and the sum of mapping qualities of
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
841 supporting reads is at least Q. default: 0
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
842 -Q --mismatch-base-quality-threshold Q
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
843 Count mismatches toward --read-mismatch-limit if the base
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
844 quality of the mismatch is >= Q. default: 10
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
845 -U --read-mismatch-limit N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
846 Exclude reads with more than N mismatches where each mismatch
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
847 has base quality >= mismatch-base-quality-threshold.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
848 default: ~unbounded
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
849 -z --read-max-mismatch-fraction N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
850 Exclude reads with more than N [0,1] fraction of mismatches where
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
851 each mismatch has base quality >= mismatch-base-quality-threshold
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
852 default: 1.0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
853 -$ --read-snp-limit N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
854 Exclude reads with more than N base mismatches, ignoring gaps
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
855 with quality >= mismatch-base-quality-threshold.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
856 default: ~unbounded
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
857 -e --read-indel-limit N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
858 Exclude reads with more than N separate gaps.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
859 default: ~unbounded
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
860 -0 --standard-filters Use stringent input base and mapping quality filters
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
861 Equivalent to -m 30 -q 20 -R 0 -S 0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
862 -F --min-alternate-fraction N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
863 Require at least this fraction of observations supporting
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
864 an alternate allele within a single individual in the
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
865 in order to evaluate the position. default: 0.2
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
866 -C --min-alternate-count N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
867 Require at least this count of observations supporting
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
868 an alternate allele within a single individual in order
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
869 to evaluate the position. default: 2
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
870 -3 --min-alternate-qsum N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
871 Require at least this sum of quality of observations supporting
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
872 an alternate allele within a single individual in order
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
873 to evaluate the position. default: 0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
874 -G --min-alternate-total N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
875 Require at least this count of observations supporting
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
876 an alternate allele within the total population in order
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
877 to use the allele in analysis. default: 1
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
878 -! --min-coverage N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
879 Require at least this coverage to process a site. default: 0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
880
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
881 Population priors::
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
882
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
883 -k --no-population-priors
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
884 Equivalent to --pooled-discrete --hwe-priors-off and removal of
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
885 Ewens Sampling Formula component of priors.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
886
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
887 Mappability priors::
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
888
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
889 -w --hwe-priors-off
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
890 Disable estimation of the probability of the combination
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
891 arising under HWE given the allele frequency as estimated
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
892 by observation frequency.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
893 -V --binomial-obs-priors-off
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
894 Disable incorporation of prior expectations about observations.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
895 Uses read placement probability, strand balance probability,
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
896 and read position (5'-3') probability.
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
897 -a --allele-balance-priors-off
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
898 Disable use of aggregate probability of observation balance between alleles
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
899 as a component of the priors.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
900
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
901 Genotype likelihoods::
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
902
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
903 --observation-bias FILE
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
904 Read length-dependent allele observation biases from FILE.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
905 The format is [length] [alignment efficiency relative to reference]
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
906 where the efficiency is 1 if there is no relative observation bias.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
907 --base-quality-cap Q
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
908 Limit estimated observation quality by capping base quality at Q.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
909 --experimental-gls
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
910 Generate genotype likelihoods using 'effective base depth' metric
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
911 qual = 1-BaseQual * 1-MapQual. Incorporate partial observations.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
912 This is the default when contamination estimates are provided.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
913 Optimized for diploid samples.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
914 --prob-contamination F
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
915 An estimate of contamination to use for all samples. default: 10e-9
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
916 --contamination-estimates FILE
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
917 A file containing per-sample estimates of contamination, such as
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
918 those generated by VerifyBamID. The format should be:
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
919 sample p(read=R|genotype=AR) p(read=A|genotype=AA)
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
920 Sample '*' can be used to set default contamination estimates.
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
921
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
922 Algorithmic features::
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
923
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
924 --report-genotype-likelihood-max
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
925 Report genotypes using the maximum-likelihood estimate provided
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
926 from genotype likelihoods.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
927 -B --genotyping-max-iterations N
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
928 Iterate no more than N times during genotyping step. default: 1000.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
929 --genotyping-max-banddepth N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
930 Integrate no deeper than the Nth best genotype by likelihood when
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
931 genotyping. default: 6.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
932 -W --posterior-integration-limits N,M
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
933 Integrate all genotype combinations in our posterior space
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
934 which include no more than N samples with their Mth best
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
935 data likelihood. default: 1,3.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
936 -N --exclude-unobserved-genotypes
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
937 Skip sample genotypings for which the sample has no supporting reads.
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
938 -S --genotype-variant-threshold N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
939 Limit posterior integration to samples where the second-best
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
940 genotype likelihood is no more than log(N) from the highest
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
941 genotype likelihood for the sample. default: ~unbounded
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
942 -j --use-mapping-quality
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
943 Use mapping quality of alleles when calculating data likelihoods.
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
944 -H --harmonic-indel-quality
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
945 Use a weighted sum of base qualities around an indel, scaled by the
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
946 distance from the indel. By default use a minimum BQ in flanking sequence.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
947 -D --read-dependence-factor N
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
948 Incorporate non-independence of reads by scaling successive
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
949 observations by this factor during data likelihood
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
950 calculations. default: 0.9
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
951 -= --genotype-qualities
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
952 Calculate the marginal probability of genotypes and report as GQ in
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
953 each sample field in the VCF output.
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
954
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
955
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
956 ------
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
957
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
958 **Acknowledgments**
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
959
2
14f952d2a9db Uploaded
devteam
parents: 0
diff changeset
960 The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
4
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
961 TNG was developed by Bjoern Gruening
c171daf263dd planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit cf4a70e780f104bc724323912b3b87fb37f887dd
devteam
parents: 3
diff changeset
962 </help>
6
3aacf7637e02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
iuc
parents: 5
diff changeset
963 <expand macro="citations" />
0
e21073b0dc1f Uploaded initial revision.
devteam
parents:
diff changeset
964 </tool>