Mercurial > repos > jjohnson > bcftools_call

comparison bcftools_call.xml @ 0:20b3aaa16d64 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/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:46:24 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:20b3aaa16d64
1 <?xml version='1.0' encoding='utf-8'?>
2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
3 <description>SNP/indel variant calling from VCF/BCF</description>
4 <macros>
5 <token name="@EXECUTABLE@">call</token>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="version_command" />
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
22 bcftools @EXECUTABLE@
23
24 #set $section = $sec_consensus_variant_calling.variant_calling
25 #if $section.method == 'multiallelic':
26 -m
27 #if str($section.gvcf) != '':
28 --gvcf $section.gvcf
29 #end if
30 #if $section.genotypes.constrain == 'alleles':
31 --constrain alleles $section.genotypes.insert_missed
32 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
33 @TARGETS_FILE@
34 #else
35 #if $section.genotypes.constrain == 'trio':
36 --constrain trio
37 #if $section.genotypes.novel_rate:
38 --novel-rate '$section.genotypes.novel_rate'
39 #end if
40 #end if
41 #set $section = $sec_consensus_variant_calling.variant_calling.genotypes
42 @TARGETS@
43 #end if
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
59
60 ## File format section
61 #set $section = $sec_file_format
62 #if $section.ploidy:
63 --ploidy "${section.ploidy}"
64 #end if
65 #if $section.ploidy_file:
66 --ploidy-file "${section.ploidy_file}"
67 #end if
68
69 ## Input/output section
70 #set $section = $sec_input_output
71 ${section.keep_alts}
72 ## #if section.format_fields:
73 ## --format-fields "${section.format_fields}"
74 ## #end if
75 ${section.keep_masked_ref}
76 #if $section.skip_variants:
77 --skip-variants "${section.skip_variants}"
78 #end if
79 ${section.variants_only}
80
81 @OUTPUT_TYPE@
82 @THREADS@
83
84 ## Primary Input/Outputs
85 @INPUT_FILE@
86 > "$output_file"
87 ]]>
88 </command>
89 <inputs>
90 <expand macro="macro_input" />
91 <section name="sec_restrict" expanded="false" title="Restrict to">
92 <expand macro="macro_regions" />
93 <expand macro="macro_samples" />
94 </section>
95 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
96 <conditional name="variant_calling">
97 <param name="method" type="select" label="calling method">
98 <option value="multiallelic">Multiallelic and rare-variant Caller</option>
99 <option value="consensus">Consensus Caller</option>
100 </param>
101 <when value="multiallelic">
102 <conditional name="genotypes">
103 <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
104 <option value="none">Do not constrain</option>
105 <option value="alleles">alleles - call genotypes given alleles</option>
106 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
107 </param>
108 <when value="none">
109 <expand macro="macro_targets" />
110 </when>
111 <when value="alleles">
112 <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" />
114 </when>
115 <when value="trio">
116 <expand macro="macro_targets" />
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" />
118 </when>
119 </conditional>
120 <param name="gvcf" type="integer" label="gvcf" optional="True" help="group non-variant sites into gVCF blocks by minimum per-sample DP" />
121 </when>
122 <when value="consensus">
123 <conditional name="genotypes">
124 <param name="constrain" type="select" label="Constrain" help="one of: alleles, trio (see manual)">
125 <option value="none">Do not constrain</option>
126 <option value="trio">trio - call genotypes given the father-mother-child constraint</option>
127 </param>
128 <when value="none">
129 </when>
130 <when value="trio">
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" />
132 </when>
133 </conditional>
134 <expand macro="macro_targets" />
135 </when>
136 </conditional>
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" />
138 <param name="prior" type="float" label="Prior" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" />
139 </section>
140 <section name="sec_file_format" expanded="false" title="File format Options">
141 <param name="ploidy" type="select" label="Select Predefined Ploidy" optional="true">
142 <option value="GRCh37">GRCh37 - Human Genome reference assembly GRCh37 / hg19</option>
143 <option value="GRCh38">GRCh37 - Human Genome reference assembly GRCh38 / hg38</option>
144 <option value="X">X - Treat male samples as haploid and female as diploid regardless of the chromosome name</option>
145 <option value="Y">Y - Treat male samples as haploid and female as no-copy, regardless of the chromosome name"</option>
146 <option value="1">1 - Treat all samples as haploid</option>
147 </param>
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" />
149 <expand macro="macro_regions" />
150 <expand macro="macro_samples" />
151 </section>
152 <section name="sec_input_output" expanded="false" title="Input/output Options">
153 <param name="keep_alts" type="boolean" truevalue="--keep-alts" falsevalue="" label="Keep Alts" help="keep all possible alternate alleles at variant sites" />
154 <param name="format_fields" type="text" value="" optional="true" label="Format Fields"
155 help="output format fields: GQ,GP" >
156 <validator type="regex" message="FORMAT terms separated by commas">^([A-Za-z]+(,[A-Za-z]+)*)?$</validator>
157 </param>
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)" />
159 <param name="skip_variants" type="select" label="Skip Variants" optional="True" help="skip indels/snps">
160 <option value="indels">indels</option>
161 <option value="snps">snps</option>
162 </param>
163 <param name="variants_only" type="boolean" truevalue="--variants-only" falsevalue="" label="Variants Only" help="output variant sites only" />
164 </section>
165 <expand macro="macro_select_output_type" />
166 </inputs>
167 <outputs>
168 <expand macro="macro_vcf_output"/>
169 </outputs>
170 <tests>
171 <test>
172 <param name="input_file" ftype="vcf" value="mpileup.vcf" />
173 <param name="method" value="multiallelic" />
174 <param name="variants_only" value="true" />
175 <param name="output_type" value="v" />
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" />
239 </tool>