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comparison bcftools_call.xml @ 2:0812cba3c4c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 06:53:57 -0400
parents dabc1e7ca486
children a4f3b1dbb345
comparison
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1:3b0006e824c6 2:0812cba3c4c8
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@.0"> 2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
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 </macros> 7 </macros>
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command detect_errors="aggressive"><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
11 @PREPARE_ENV@
12 @PREPARE_INPUT_FILE@
13 #set $section = $sec_consensus_variant_calling.variant_calling
14 #set $targets_path = None
15 #if $section.method == 'multiallelic':
16 #if $section.genotypes.constrain == 'alleles':
17 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
18 @PREPARE_TARGETS_FILE@
19 #end if
20 #end if
21
11 bcftools @EXECUTABLE@ 22 bcftools @EXECUTABLE@
12 23
13 ## Consensus/variant calling section 24 #set $section = $sec_consensus_variant_calling.variant_calling
14 #if $sec_consensus_variant_calling.select_caller == "consensus": 25 #if $section.method == 'multiallelic':
15 --consensus-caller 26 -m
16 #else: 27 #if str($section.gvcf) != '':
17 --multiallelic-caller 28 --gvcf $section.gvcf
18 #end if 29 #end if
19 30 #if $section.genotypes.constrain == 'alleles':
20 #if $sec_consensus_variant_calling.constraints.constrain_select == "alleles": 31 --constrain alleles $section.genotypes.insert_missed
21 --constrain alleles 32 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
22 #elif $sec_consensus_variant_calling.constraints.constrain_select == "trio": 33 @TARGETS_FILE@
23 --constrain trio 34 #else
24 --novel-rate ${sec_consensus_variant_calling.constraints.novel_snp},${sec_consensus_variant_calling.constraints.novel_ins},${sec_consensus_variant_calling.constraints.novel_del} 35 #if $section.genotypes.constrain == 'trio':
25 --pval-threshold "${sec_consensus_variant_calling.constraints.pval_threshold}" 36 --constrain trio
26 #end if 37 #if $section.genotypes.novel_rate:
27 38 --novel-rate '$section.genotypes.novel_rate'
28 #if $sec_consensus_variant_calling.prior: 39 #end if
29 --prior "${sec_consensus_variant_calling.prior}" 40 #end if
30 #end if 41 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
31 ${sec_consensus_variant_calling.chromosome_X} 42 @TARGETS@
32 ${sec_consensus_variant_calling.chromosome_Y} 43 #end if
33 44 #else
45 -c
46 #end if
47
48 #set $section = $sec_restrict
49 @REGIONS@
50 @SAMPLES@
51
52 #set $section = $sec_consensus_variant_calling
53 #if $section.pval_threshold:
54 --pval-threshold "$section.pval_threshold"
55 #end if
56 #if $section.prior:
57 --prior "$section.prior"
58 #end if
34 59
35 ## File format section 60 ## File format section
36 #if str($sec_default.select_output_type) != "__none__": 61 #set $section = $sec_file_format
37 --output-type "${sec_default.select_output_type}" 62 #if $section.ploidy:
38 #end if 63 --ploidy "${section.ploidy}"
39 @SEC_DEF_REGIONS@ 64 #end if
40 @SEC_DEF_SAMPLES@ 65 #if $section.ploidy_file:
41 @SEC_DEF_TARGETS@ 66 --ploidy-file "${section.ploidy_file}"
42 67 #end if
43 68
44 ## Input/output section 69 ## Input/output section
45 ${sec_input_output.keep_alts} 70 #set $section = $sec_input_output
46 #set values_sec_input_output_format_fields = '","'.join([str($value) for $value in $sec_input_output.format_fields_repeat]) 71 ${section.keep_alts}
47 #if $values_sec_input_output_format_fields: 72 ## #if section.format_fields:
48 --format-fields "${values_sec_input_output_format_fields}" 73 ## --format-fields "${section.format_fields}"
49 #end if 74 ## #end if
50 75 ${section.keep_masked_ref}
51 #if str($sec_input_output.gvcf) != "": 76 #if $section.skip_variants:
52 --gvcf "${sec_input_output.gvcf}" 77 --skip-variants "${section.skip_variants}"
53 #end if 78 #end if
54 79 ${section.variants_only}
55 ${sec_input_output.insert_missed} 80
56 ${sec_input_output.keep_masked_ref} 81 @OUTPUT_TYPE@
57 82 @THREADS@
58 #if str($sec_input_output.skip_variants) != "__none__":
59 --skip-variants "${sec_input_output.skip_variants}"
60 #end if
61
62 ${sec_input_output.variants_only}
63 83
64 ## Primary Input/Outputs 84 ## Primary Input/Outputs
65 85 @INPUT_FILE@
66 $input_file 86 > "$output_file"
67 >
68 $output_file
69 ]]> 87 ]]>
70 </command> 88 </command>
71 <inputs> 89 <inputs>
72 <param name="input_file" label="VCF/BCF Data" type="data" format="vcf,bcf,vcf_bgz,bcf_bgz" /> 90 <expand macro="macro_input" />
73 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options"> 91 <section name="sec_restrict" expanded="false" title="Restrict to">
74 <param name="select_caller" label="Calling Method" type="select"> 92 <expand macro="macro_regions" />
75 <option value="consensus">the original calling method (-c, --consensus-caller)</option> 93 <expand macro="macro_samples" />
76 <option value="multiallelic">alternative model for multiallelic and rare-variant calling (-m, --multiallelic-caller)</option> 94 </section>
77 </param> 95 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
78 <conditional name="constraints" label="Constraints"> 96 <conditional name="variant_calling">
79 <param name="constrain_select" label="Constraints" type="select" argument="-C"> 97 <param name="method" type="select" label="calling method">
80 <option value="__none__" selected="True">No constraints</option> 98 <option value="multiallelic">Multiallelic and rare-variant Caller</option>
81 <option value="alleles">call genotypes given alleles (alleles)</option> 99 <option value="consensus">Consensus Caller</option>
82 <option value="trio">call genotypes given the father-mother-child constraint (trio)</option> 100 </param>
83 </param> 101 <when value="multiallelic">
84 <when value="__none__" /> 102 <conditional name="genotypes">
85 <when value="alleles" /> 103 <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
86 <when value="trio"> 104 <option value="none">Do not constrain</option>
87 <param name="novel_snp" label="Novel Rate: SNPs" type="float" default="1e-8" optional="True" help="mutation rate of SNPs" argument="--novel-rate"/> 105 <option value="alleles">alleles - call genotypes given alleles</option>
88 <param name="novel_ins" label="Novel Rate: Insertions" type="float" default="1e-9" optional="True" help="mutation rate of insertions according to their length" argument="--novel-rate" /> 106 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
89 <param name="novel_del" label="Novel Rate: Deletions" type="float" default="1e-9" optional="True" help="mutation rate of deletions according to their length" argument="--novel-rate" /> 107 </param>
90 <param name="pval_threshold" label="Pval Threshold" type="float" default="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" argument="--pval-treshold"/> 108 <when value="none">
91 </when> 109 <expand macro="macro_targets" />
92 </conditional> 110 </when>
93 <param name="prior" label="Prior" type="float" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" argument="--prior" /> 111 <when value="alleles">
94 <param name="chromosome_X" label="Chromosome X" type="boolean" truevalue="--chromosome-X" falsevalue="" help="haploid output for male samples (requires PED file with -s)" argument="--chromosome-X"/> 112 <expand macro="macro_targets_file"/>
95 <param name="chromosome_Y" label="Chromosome Y" type="boolean" truevalue="--chromosome-Y" falsevalue="" help="haploid output for males and skips females (requires PED file with -s)" argument="--chromosome-Y"/> 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" />
96 </section> 114 </when>
97 <section name="sec_default" expanded="true" title="Default Options"> 115 <when value="trio">
98 <expand macro="macro_select_output_type" /> 116 <expand macro="macro_targets" />
99 <expand macro="macro_regions" /> 117 <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
100 <expand macro="macro_samples" /> 118 </when>
101 <expand macro="macro_targets" /> 119 </conditional>
102 </section> 120 <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
103 <section name="sec_input_output" expanded="true" title="Input/output Options"> 121 </when>
104 <param name="keep_alts" label="Keep Alts" type="boolean" truevalue="--keep-alts" falsevalue="" help="keep all possible alternate alleles at variant sites" argument="--keep-alts"/> 122 <when value="consensus">
105 <repeat name="format_fields_repeat" title="Format Fields"> 123 <conditional name="genotypes">
106 <param name="format_fields" type="text" label="Format Fields" help="output format fields: e.g. GQ, GP (lowercase allowed)" argument="--format-fields" /> 124 <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
107 </repeat> 125 <option value="none">Do not constrain</option>
108 <param name="gvcf" label="Gvcf" type="integer" optional="True" help="output gVCF blocks of homozygous REF calls. The parameter is the minimum per-sample depth required to include a site in the non-variant block." argument="--gvcf"/> 126 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
109 <param name="insert_missed" label="Insert Missed" type="boolean" truevalue="--insert-missed" falsevalue="" help="output also sites missed by mpileup but present in -T" argument="--insert-missed"/> 127 </param>
110 <param name="keep_masked_ref" label="Keep Masked Ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" help="keep sites with masked reference allele (REF=N)" argument="--keep-masked-ref"/> 128 <when value="none">
111 <param name="skip_variants" label="Skip Variants" type="select" help="Skip indels/SNP sites" argument="--skip-variants"> 129 </when>
112 <option value="__none__" selected="True">Don't skip any</option> 130 <when value="trio">
113 <option value="indels">Skip indels</option> 131 <param name="novel_rate" type="float" label="Novel Rate" default="1e-8,1e-9,1e-9" optional="true" help="likelihood of novel mutation for constrained trio calling, see man page for details" />
114 <option value="snps">Skip snps</option> 132 </when>
115 </param> 133 </conditional>
116 <param name="variants_only" label="Variants Only" type="boolean" truevalue="--variants-only" falsevalue="" help="output variant sites only" argument="--variants-only"/> 134 <expand macro="macro_targets" />
117 </section> 135 </when>
118 </inputs> 136 </conditional>
119 <outputs> 137 <param name="pval_threshold" type="float" label="Pval Threshold" default="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" />
120 <data name="output_file" format="vcf"> 138 <param name="prior" type="float" label="Prior" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
121 <change_format> 139 </section>
122 <when input="sec_file_format|select_output_type" value="b" format="bcf_bgz" /> 140 <section name="sec_file_format" expanded="false" title="File format Options">
123 <when input="sec_file_format|select_output_type" value="u" format="bcf" /> 141 <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true">
124 <when input="sec_file_format|select_output_type" value="z" format="vcf_bgz" /> 142 <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option>
125 <when input="sec_file_format|select_output_type" value="v" format="vcf" /> 143 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>
126 </change_format> 144 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
127 </data> 145 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
128 </outputs> 146 <option value="1">1 - Treat all samples as haploid</option>
129 <tests> 147 </param>
130 <test> 148 <param name="ploidy_file" type="data" format="tabular" label="Ploidy File" optional="True" help="space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY" />
131 <param name="input_file" value="mpileup.vcf" /> 149 <expand macro="macro_regions" />
132 <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" /> 150 <expand macro="macro_samples" />
133 <param name="sec_input_output|variants_only" value="--variants-only" /> 151 </section>
134 <param name="sec_file_format|select_output_type" value="v" /> 152 <section name="sec_input_output" expanded="false" title="Input/output Options">
135 <output name="output_file" file="mpileup.1.out" lines_diff="2" ftype="vcf" /> 153 <param name="keep_alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep Alts" help="keep all possible alternate alleles at variant sites" />
136 </test> 154 <param name="format_fields" type="text" value="" optional="true" label="Format Fields"
137 <test> 155 help="output format fields: GQ,GP" >
138 <param name="input_file" value="mpileup.vcf" /> 156 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>
139 <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" /> 157 </param>
140 <param name="sec_input_output|variants_only" value="--variants-only" /> 158 <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)" />
141 <param name="sec_input_output|gvcf" value="0" /> 159 <param name="skip_variants" type="select" label="Skip Variants" optional="True" help="skip indels/snps">
142 <param name="sec_file_format|select_output_type" value="v" /> 160 <option value="indels">indels</option>
143 <output name="output_file" file="mpileup.2.out" lines_diff="2" ftype="vcf" /> 161 <option value="snps">snps</option>
144 </test> 162 </param>
145 </tests> 163 <param name="variants_only" type="boolean" truevalue="--variants-only" falsevalue="" label="Variants Only" help="output variant sites only" />
146 <help> 164 </section>
147 <![CDATA[ 165 <expand macro="macro_select_output_type" />
148 **bcftools call** 166 </inputs>
149 167 <outputs>
150 SNP/indel variant calling from VCF/BCF. To be used in conjunction with 168 <expand macro="macro_vcf_output"/>
151 samtools mpileup. This command replaces the former "bcftools view" 169 </outputs>
152 caller. Some of the original functionality has been temporarily lost in 170 <tests>
153 the process of transition to htslib, but will be added back on popular 171 <test>
154 demand. The original calling model can be invoked with the -c 172 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
155 option. 173 <param name="method" value="multiallelic" />
156 ]]> 174 <param name="variants_only" value="true" />
157 </help> 175 <param name="output_type" value="v" />
158 <expand macro="citations" /> 176 <output name="output_file">
177 <assert_contents>
178 <has_text text="DP4=2,4,8,11;MQ=49" />
179 </assert_contents>
180 </output>
181 </test>
182 <test>
183 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
184 <param name="method" value="multiallelic" />
185 <param name="gvcf" value="0" />
186 <param name="output_type" value="v" />
187 <output name="output_file">
188 <assert_contents>
189 <has_text text="MinDP" />
190 <has_text text="DP4=2,4,8,11;MQ=49" />
191 </assert_contents>
192 </output>
193 </test>
194 <test>
195 <param name="input_file" ftype="vcf" value="mpileup.X.vcf" />
196 <param name="method" value="multiallelic" />
197 <param name="ploidy_file" value="mpileup.ploidy" />
198 <param name="samples_file" value="mpileup.samples" />
199 <param name="output_type" value="v" />
200 <output name="output_file">
201 <assert_contents>
202 <has_text text="DP4=2,4,8,11;MQ=49" />
203 </assert_contents>
204 </output>
205 </test>
206 <test>
207 <param name="input_file" ftype="vcf" value="mpileup.X.vcf" />
208 <param name="method" value="consensus" />
209 <param name="output_type" value="v" />
210 <param name="ploidy_file" value="mpileup.ploidy" />
211 <output name="output_file">
212 <assert_contents>
213 <has_text text="DP4=2,4,8,11" />
214 <has_text text="PV4=1,1,1,1" />
215 </assert_contents>
216 </output>
217 </test>
218 </tests>
219 <help><![CDATA[
220 ==================================
221 bcftools @EXECUTABLE@
222 ==================================
223
224 SNP/indel variant calling from VCF/BCF. To be used in conjunction with samtools mpileup.
225
226 - 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.
228 - The original calling model can be invoked with the -c option.
229
230 @REGIONS_HELP@
231 @TARGETS_HELP@
232
233 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
234
235 @BCFTOOLS_WIKI@
236 ]]>
237 </help>
238 <expand macro="citations" />
159 </tool> 239 </tool>