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comparison bcftools_call.xml @ 6:3296c3680d96 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:43:02 -0400
parents 0a564427739d
children 0fba2c15b40d
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5:0a564427739d 6:3296c3680d96
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="1.3.2.0"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@">
3 <description>SNP/indel variant calling from VCF/BCF</description> 3 <description>SNP/indel variant calling from VCF/BCF</description>
4 <macros> 4 <macros>
5 <token name="@EXECUTABLE@">call</token> 5 <token name="@EXECUTABLE@">call</token>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <xml name="macro_novel_rate"> 7 <xml name="macro_novel_rate">
39 #if $section.genotypes.constrain == 'alleles': 39 #if $section.genotypes.constrain == 'alleles':
40 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes 40 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
41 @PREPARE_TARGETS_FILE@ 41 @PREPARE_TARGETS_FILE@
42 #end if 42 #end if
43 #end if 43 #end if
44 #set $section = $sec_restrict
45 @PREPARE_REGIONS_FILE@
44 46
45 bcftools @EXECUTABLE@ 47 bcftools @EXECUTABLE@
46 48
47 #set $section = $sec_consensus_variant_calling.variant_calling 49 #set $section = $sec_consensus_variant_calling.variant_calling
48 #if $section.method == 'multiallelic': 50 #if $section.method == 'multiallelic':
49 -m 51 -m
50 #if str($section.gvcf) != '': 52 #if str($section.gvcf) != '':
51 --gvcf $section.gvcf 53 --gvcf $section.gvcf
54 #end if
55 #if str($section.prior_freqs) != '':
56 --prior-freqs $section.prior_freqs
52 #end if 57 #end if
53 #if $section.genotypes.constrain == 'alleles': 58 #if $section.genotypes.constrain == 'alleles':
54 --constrain alleles $section.genotypes.insert_missed 59 --constrain alleles $section.genotypes.insert_missed
55 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes 60 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
56 @TARGETS_FILE@ 61 @TARGETS_FILE@
102 @OUTPUT_TYPE@ 107 @OUTPUT_TYPE@
103 @THREADS@ 108 @THREADS@
104 109
105 ## Primary Input/Outputs 110 ## Primary Input/Outputs
106 @INPUT_FILE@ 111 @INPUT_FILE@
107 > "$output_file" 112 > '$output_file'
108 ]]> 113 ]]>
109 </command> 114 </command>
110 <inputs> 115 <inputs>
111 <expand macro="macro_input" /> 116 <expand macro="macro_input" />
112 <section name="sec_restrict" expanded="false" title="Restrict to"> 117 <section name="sec_restrict" expanded="false" title="Restrict to">
136 <when value="trio"> 141 <when value="trio">
137 <expand macro="macro_targets" /> 142 <expand macro="macro_targets" />
138 <expand macro="macro_novel_rate" /> 143 <expand macro="macro_novel_rate" />
139 </when> 144 </when>
140 </conditional> 145 </conditional>
146 <param name="prior_freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
147 <help>
148 <![CDATA[
149 For example: --prior-freqs REF_AN,REF_AC
150 <br>if the input VCF has the following INFO tags:
151 <br>##INFO=&lt;ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes"&gt;
152 <br>##INFO=&lt;ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele"&gt;
153 ]]>
154 </help>
155 <validator type="regex" message="The INFO tags (separated by a comma), e.g. AN,AC">^(\w+,\w+)?$</validator>
156 </param>
141 <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" /> 157 <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
142 </when> 158 </when>
143 <when value="consensus"> 159 <when value="consensus">
144 <conditional name="genotypes"> 160 <conditional name="genotypes">
145 <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)"> 161 <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
248 - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand. 264 - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand.
249 - The original calling model can be invoked with the -c option. 265 - The original calling model can be invoked with the -c option.
250 266
251 The novel-rate option can be set to modify the likelihood of novel mutation for constrained -C trio calling. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn). By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value is given, the same mutation rate Pn is used for SNPs and indels. 267 The novel-rate option can be set to modify the likelihood of novel mutation for constrained -C trio calling. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn). By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=float*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value is given, the same mutation rate Pn is used for SNPs and indels.
252 268
269
253 @REGIONS_HELP@ 270 @REGIONS_HELP@
254 @TARGETS_HELP@ 271 @TARGETS_HELP@
255 272
256 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 273 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
257 274