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comparison bcftools_call.xml @ 4:6d2a5f0859cf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9df9b52baf62b70fbcfc3fbe965d7197d4e8738e
author iuc
date Tue, 31 Jan 2017 12:41:31 -0500
parents 5337db17a5f7
children 0a564427739d
comparison
equal deleted inserted replaced
3:5337db17a5f7 4:6d2a5f0859cf
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="@VERSION@.1"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.2">
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">
8 <param name="novel_rate_snp" type="float" label="Novel Rate SNP" value="" optional="true"
9 help="likelihood of novel mutation for constrained trio calling, see man page for details" />
10 <param name="novel_rate_del" type="float" label="Novel Rate Deletions" value="" optional="true"
11 help="likelihood of novel mutation for constrained trio calling, see man page for details" />
12 <param name="novel_rate_ins" type="float" label="Novel Rate Insertions" value="" optional="true"
13 help="likelihood of novel mutation for constrained trio calling, see man page for details" />
14 </xml>
15 <token name="@NOVEL_RATE@">
16 #set $novel_rate = []
17 #if str($section.genotypes.novel_rate_snp):
18 #silent $novel_rate.append(str($section.genotypes.novel_rate_snp))
19 #end if
20 #if str($section.genotypes.novel_rate_del):
21 #silent $novel_rate.append(str($section.genotypes.novel_rate_del))
22 #end if
23 #if str($section.genotypes.novel_rate_ins):
24 #silent $novel_rate.append(str($section.genotypes.novel_rate_ins))
25 #end if
26 #if len($novel_rate) > 0:
27 --novel-rate '#echo ','.join($novel_rate)#'
28 #end if
29 </token>
7 </macros> 30 </macros>
8 <expand macro="requirements" /> 31 <expand macro="requirements" />
9 <expand macro="version_command" /> 32 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[ 33 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@ 34 @PREPARE_ENV@
32 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes 55 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
33 @TARGETS_FILE@ 56 @TARGETS_FILE@
34 #else 57 #else
35 #if $section.genotypes.constrain == 'trio': 58 #if $section.genotypes.constrain == 'trio':
36 --constrain trio 59 --constrain trio
37 #if $section.genotypes.novel_rate: 60 @NOVEL_RATE@
38 --novel-rate '$section.genotypes.novel_rate'
39 #end if
40 #end if 61 #end if
41 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes 62 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
42 @TARGETS@ 63 @TARGETS@
43 #end if 64 #end if
44 #else 65 #else
112 <expand macro="macro_targets_file"/> 133 <expand macro="macro_targets_file"/>
113 <param name="insert_missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert Missed" help="output also sites missed by mpileup but present in -T" /> 134 <param name="insert_missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert Missed" help="output also sites missed by mpileup but present in -T" />
114 </when> 135 </when>
115 <when value="trio"> 136 <when value="trio">
116 <expand macro="macro_targets" /> 137 <expand macro="macro_targets" />
117 <param name="novel_rate" type="float" label="Novel Rate" value="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" /> 138 <expand macro="macro_novel_rate" />
118 </when> 139 </when>
119 </conditional> 140 </conditional>
120 <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" /> 141 <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
121 </when> 142 </when>
122 <when value="consensus"> 143 <when value="consensus">
126 <option value="trio">trio - call genotypes given the father-mother-child constraint</option> 147 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
127 </param> 148 </param>
128 <when value="none"> 149 <when value="none">
129 </when> 150 </when>
130 <when value="trio"> 151 <when value="trio">
131 <param name="novel_rate" type="float" label="Novel Rate" value="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" /> 152 <expand macro="macro_novel_rate" />
132 </when> 153 </when>
133 </conditional> 154 </conditional>
134 <expand macro="macro_targets" /> 155 <expand macro="macro_targets" />
135 </when> 156 </when>
136 </conditional> 157 </conditional>
225 246
226 - This command replaces the former "bcftools view" caller. 247 - This command replaces the former "bcftools view" caller.
227 - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand. 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.
228 - The original calling model can be invoked with the -c option. 249 - The original calling model can be invoked with the -c option.
229 250
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.
252
230 @REGIONS_HELP@ 253 @REGIONS_HELP@
231 @TARGETS_HELP@ 254 @TARGETS_HELP@
232 255
233 @BCFTOOLS_MANPAGE@#@EXECUTABLE@ 256 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
234 257