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comparison bcftools_call.xml @ 8:0fba2c15b40d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
author iuc
date Thu, 21 Feb 2019 16:09:28 -0500
parents 3296c3680d96
children cb30a39055d0
comparison
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7:b03984136ce4 8:0fba2c15b40d
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@"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_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">
8 <param name="novel_rate_snp" type="float" label="Novel Rate SNP" value="" optional="true" 8 <param name="novel_rate_snp" type="float" value="" optional="true" label="Novel rate for SNPs"
9 help="likelihood of novel mutation for constrained trio calling, see man page for details" /> 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" 10 <param name="novel_rate_del" type="float" value="" optional="true" label="Novel rate for deletions"
11 help="likelihood of novel mutation for constrained trio calling, see man page for details" /> 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" 12 <param name="novel_rate_ins" type="float" value="" optional="true" label="Novel rate for insertions"
13 help="likelihood of novel mutation for constrained trio calling, see man page for details" /> 13 help="Likelihood of novel mutation for constrained trio calling, see man page for details" />
14 </xml> 14 </xml>
15 <token name="@NOVEL_RATE@"> 15 <token name="@NOVEL_RATE@">
16 #set $novel_rate = [] 16 #set $novel_rate = []
17 #if str($section.genotypes.novel_rate_snp): 17 #if str($section.genotypes.novel_rate_snp):
18 #silent $novel_rate.append(str($section.genotypes.novel_rate_snp)) 18 #silent $novel_rate.append(str($section.genotypes.novel_rate_snp))
34 @PREPARE_ENV@ 34 @PREPARE_ENV@
35 @PREPARE_INPUT_FILE@ 35 @PREPARE_INPUT_FILE@
36 #set $section = $sec_consensus_variant_calling.variant_calling 36 #set $section = $sec_consensus_variant_calling.variant_calling
37 #set $targets_path = None 37 #set $targets_path = None
38 #if $section.method == 'multiallelic': 38 #if $section.method == 'multiallelic':
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 44 #set $section = $sec_restrict
45 @PREPARE_REGIONS_FILE@ 45 @PREPARE_REGIONS_FILE@
46 46
47 bcftools @EXECUTABLE@ 47 bcftools @EXECUTABLE@
48 48
49 #set $section = $sec_consensus_variant_calling.variant_calling 49 #set $section = $sec_consensus_variant_calling.variant_calling
50 #if $section.method == 'multiallelic': 50 #if $section.method == 'multiallelic':
51 -m 51 -m
52 #if str($section.gvcf) != '': 52 #if str($section.gvcf):
53 --gvcf $section.gvcf 53 --gvcf $section.gvcf
54 #end if 54 #end if
55 #if str($section.prior_freqs) != '': 55 #if str($section.prior_freqs):
56 --prior-freqs $section.prior_freqs 56 --prior-freqs '$section.prior_freqs'
57 #end if 57 #end if
58 #if $section.genotypes.constrain == 'alleles': 58 #if str($section.prior):
59 --constrain alleles $section.genotypes.insert_missed 59 --prior $section.prior
60 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes 60 #end if
61 @TARGETS_FILE@ 61 #if $section.genotypes.constrain == 'alleles':
62 #else 62 --constrain alleles $section.genotypes.insert_missed
63 #if $section.genotypes.constrain == 'trio': 63 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
64 --constrain trio 64 @TARGETS_FILE@
65 @NOVEL_RATE@ 65 #else
66 #end if 66 #if $section.genotypes.constrain == 'trio':
67 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes 67 --constrain trio
68 @TARGETS@ 68 @NOVEL_RATE@
69 #end if 69 #end if
70 #else 70 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
71 -c 71 @TARGETS@
72 #end if
73 #else
74 -c
75 #if str($section.pval_threshold):
76 --pval-threshold $section.pval_threshold
77 #end if
72 #end if 78 #end if
73 79
74 #set $section = $sec_restrict 80 #set $section = $sec_restrict
75 @REGIONS@ 81 @REGIONS@
76 @SAMPLES@ 82 @SAMPLES@
77 83
78 #set $section = $sec_consensus_variant_calling
79 #if $section.pval_threshold:
80 --pval-threshold "$section.pval_threshold"
81 #end if
82 #if $section.prior:
83 --prior "$section.prior"
84 #end if
85
86 ## File format section 84 ## File format section
87 #set $section = $sec_file_format 85 #set $section = $sec_file_format
88 #if $section.ploidy: 86 #if $section.ploidy:
89 --ploidy "${section.ploidy}" 87 --ploidy ${section.ploidy}
90 #end if 88 #end if
91 #if $section.ploidy_file: 89 #if $section.ploidy_file:
92 --ploidy-file "${section.ploidy_file}" 90 --ploidy-file '${section.ploidy_file}'
93 #end if 91 #end if
94 92
95 ## Input/output section 93 ## Input/output section
96 #set $section = $sec_input_output 94 #set $section = $sec_input_output
97 ${section.keep_alts} 95 ${section.keep_alts}
98 ## #if section.format_fields: 96 #if $section.format_fields:
99 ## --format-fields "${section.format_fields}" 97 --format-fields '${section.format_fields}'
100 ## #end if 98 #end if
101 ${section.keep_masked_ref} 99 ${section.keep_masked_ref}
102 #if $section.skip_variants: 100 #if $section.skip_variants:
103 --skip-variants "${section.skip_variants}" 101 --skip-variants ${section.skip_variants}
104 #end if 102 #end if
105 ${section.variants_only} 103 ${section.variants_only}
106 104
107 @OUTPUT_TYPE@ 105 @OUTPUT_TYPE@
108 @THREADS@ 106 @THREADS@
109 107
110 ## Primary Input/Outputs 108 ## Primary Input/Outputs
111 @INPUT_FILE@ 109 @INPUT_FILE@
112 > '$output_file' 110 > '$output_file'
113 ]]> 111 ]]></command>
114 </command>
115 <inputs> 112 <inputs>
116 <expand macro="macro_input" /> 113 <expand macro="macro_input" />
117 <section name="sec_restrict" expanded="false" title="Restrict to"> 114 <section name="sec_restrict" expanded="false" title="Restrict to">
118 <expand macro="macro_regions" /> 115 <expand macro="macro_regions" />
119 <expand macro="macro_samples" /> 116 <expand macro="macro_samples" />
120 </section> 117 </section>
121 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options"> 118 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
122 <conditional name="variant_calling"> 119 <conditional name="variant_calling">
123 <param name="method" type="select" label="calling method"> 120 <param name="method" type="select" label="Calling method">
124 <option value="multiallelic">Multiallelic and rare-variant Caller</option> 121 <option value="multiallelic">Multiallelic and rare-variant caller</option>
125 <option value="consensus">Consensus Caller</option> 122 <option value="consensus">Consensus caller</option>
126 </param> 123 </param>
127 <when value="multiallelic"> 124 <when value="multiallelic">
128 <conditional name="genotypes"> 125 <conditional name="genotypes">
129 <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)"> 126 <param argument="--constrain" type="select" label="Constrain" help="One of: alleles, trio (see manual)">
130 <option value="none">Do not constrain</option> 127 <option value="none">Do not constrain</option>
131 <option value="alleles">alleles - call genotypes given alleles</option> 128 <option value="alleles">alleles - call genotypes given alleles</option>
132 <option value="trio">trio - call genotypes given the father-mother-child constraint</option> 129 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
133 </param> 130 </param>
134 <when value="none"> 131 <when value="none">
135 <expand macro="macro_targets" /> 132 <expand macro="macro_targets" />
136 </when> 133 </when>
137 <when value="alleles"> 134 <when value="alleles">
138 <expand macro="macro_targets_file"/> 135 <expand macro="macro_targets_file"/>
139 <param name="insert_missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert Missed" help="output also sites missed by mpileup but present in -T" /> 136 <param name="insert_missed" argument="--insert-missed" type="boolean" truevalue="--insert-missed" falsevalue="" label="Insert missed" help="Output also sites missed by mpileup but present in -T" />
140 </when> 137 </when>
141 <when value="trio"> 138 <when value="trio">
142 <expand macro="macro_targets" /> 139 <expand macro="macro_targets" />
143 <expand macro="macro_novel_rate" /> 140 <expand macro="macro_novel_rate" />
144 </when> 141 </when>
145 </conditional> 142 </conditional>
146 <param name="prior_freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies"> 143 <param name="prior_freqs" argument="--prior-freqs" type="text" value="" optional="true" label="Use prior knowledge of population allele frequencies">
147 <help> 144 <help>
148 <![CDATA[ 145 <![CDATA[
149 For example: --prior-freqs REF_AN,REF_AC 146 For example: --prior-freqs REF_AN,REF_AC
150 <br>if the input VCF has the following INFO tags: 147 <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; 148 <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; 149 <br>##INFO=&lt;ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele"&gt;
153 ]]> 150 ]]>
154 </help> 151 </help>
155 <validator type="regex" message="The INFO tags (separated by a comma), e.g. AN,AC">^(\w+,\w+)?$</validator> 152 <validator type="regex" message="The INFO tags (separated by a comma), e.g. AN,AC">^(\w+,\w+)?$</validator>
156 </param> 153 </param>
157 <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" /> 154 <param argument="--prior" type="float" value="1.1e-3" optional="true" label="Prior" help="Expected substitution rate" />
155 <param argument="--gvcf" type="integer" optional="true" label="Output also gVCF blocks of homozygous REF calls" help="The parameter value is the minimum per-sample depth required to include a site in the non-variant block" />
158 </when> 156 </when>
159 <when value="consensus"> 157 <when value="consensus">
160 <conditional name="genotypes"> 158 <conditional name="genotypes">
161 <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)"> 159 <param argument="--constrain" type="select" label="Constrain" help="One of: alleles, trio (see manual)">
162 <option value="none">Do not constrain</option> 160 <option value="none">Do not constrain</option>
163 <option value="trio">trio - call genotypes given the father-mother-child constraint</option> 161 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
164 </param> 162 </param>
165 <when value="none"> 163 <when value="none" />
166 </when>
167 <when value="trio"> 164 <when value="trio">
168 <expand macro="macro_novel_rate" /> 165 <expand macro="macro_novel_rate" />
169 </when> 166 </when>
170 </conditional> 167 </conditional>
171 <expand macro="macro_targets" /> 168 <expand macro="macro_targets" />
169 <param name="pval_threshold" argument="--pval-threshold" type="float" value="0.5" optional="true" label="Pval Threshold" help="Accept variant if P(ref|D)&lt;FLOAT" />
172 </when> 170 </when>
173 </conditional> 171 </conditional>
174 <param name="pval_threshold" type="float" label="Pval Threshold" value="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" />
175 <param name="prior" type="float" label="Prior" value="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
176 </section> 172 </section>
177 <section name="sec_file_format" expanded="false" title="File format Options"> 173 <section name="sec_file_format" expanded="false" title="File format Options">
178 <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true"> 174 <param argument="--ploidy" type="select" optional="true" label="Select predefined ploidy">
179 <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option> 175 <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option>
180 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option> 176 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>
181 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option> 177 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
182 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option> 178 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
183 <option value="1">1 - Treat all samples as haploid</option> 179 <option value="1">1 - Treat all samples as haploid</option>
184 </param> 180 </param>
185 <param name="ploidy_file" type="data" format="tabular" label="Ploidy File" optional="True" help="space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" /> 181 <param name="ploidy_file" argument="--ploidy-file" type="data" format="tabular" optional="true" label="Ploidy file" help="Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
186 <expand macro="macro_regions" /> 182 <expand macro="macro_regions" />
187 <expand macro="macro_samples" /> 183 <expand macro="macro_samples" />
188 </section> 184 </section>
189 <section name="sec_input_output" expanded="false" title="Input/output Options"> 185 <section name="sec_input_output" expanded="false" title="Input/output Options">
190 <param name="keep_alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep Alts" help="keep all possible alternate alleles at variant sites" /> 186 <param name="keep_alts" argument="--keep-alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep alts" help="Output all alternate alleles present in the alignments even if they do not appear in any of the genotypes" />
191 <param name="format_fields" type="text" value="" optional="true" label="Format Fields" 187 <param name="format_fields" argument="--format-fields" type="text" value="" optional="true" label="Comma-separated list of FORMAT fields to output for each sample"
192 help="output format fields: GQ,GP" > 188 help="Currently GQ and GP fields are supported" >
193 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator> 189 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>
194 </param> 190 </param>
195 <param name="keep_masked_ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep Masked Ref" help="keep sites with masked reference allele (REF=N)" /> 191 <param name="keep_masked_ref" argument="--keep-masked-ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" label="Keep masked reference alleles" help="Output sites where REF allele is N" />
196 <param name="skip_variants" type="select" label="Skip Variants" optional="True" help="skip indels/snps"> 192 <param name="skip_variants" argument="--skip-variants" type="select" optional="true" label="Skip variants" help="Skip indels/SNP sites">
197 <option value="indels">indels</option> 193 <option value="indels">indels</option>
198 <option value="snps">snps</option> 194 <option value="snps">snps</option>
199 </param> 195 </param>
200 <param name="variants_only" type="boolean" truevalue="--variants-only" falsevalue="" label="Variants Only" help="output variant sites only" /> 196 <param name="variants_only" argument="--variants-only" type="boolean" truevalue="--variants-only" falsevalue="" label="Output variant sites only" />
201 </section> 197 </section>
202 <expand macro="macro_select_output_type" /> 198 <expand macro="macro_select_output_type" />
203 </inputs> 199 </inputs>
204 <outputs> 200 <outputs>
205 <expand macro="macro_vcf_output"/> 201 <expand macro="macro_vcf_output"/>
256 <help><![CDATA[ 252 <help><![CDATA[
257 ================================== 253 ==================================
258 bcftools @EXECUTABLE@ 254 bcftools @EXECUTABLE@
259 ================================== 255 ==================================
260 256
261 SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup. 257 SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup.
262 258
263 - This command replaces the former "bcftools view" caller. 259 - This command replaces the former "bcftools view" caller.
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. 260 - Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand.
265 - The original calling model can be invoked with the -c option. 261 - The original calling model can be invoked with the -c option.
266 262
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. 263 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.
268 264
269 265
270 @REGIONS_HELP@ 266 @REGIONS_HELP@
271 @TARGETS_HELP@ 267 @TARGETS_HELP@
272 268