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comparison bcftools_call.xml @ 0:a531317a3527 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
author iuc
date Mon, 02 May 2016 17:27:10 -0400
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children 8959eda17fca
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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 bcftools @EXECUTABLE@
12
13 ## Consensus/variant calling section
14 #if $sec_consensus_variant_calling.select_caller == "consensus":
15 --consensus-caller
16 #else:
17 --multiallelic-caller
18 #end if
19
20 #if $sec_consensus_variant_calling.constraints.constrain_select == "alleles":
21 --constrain alleles
22 #elif $sec_consensus_variant_calling.constraints.constrain_select == "trio":
23 --constrain trio
24 --novel-rate ${sec_consensus_variant_calling.constraints.novel_snp},${sec_consensus_variant_calling.constraints.novel_ins},${sec_consensus_variant_calling.constraints.novel_del}
25 --pval-threshold "${sec_consensus_variant_calling.constraints.pval_threshold}"
26 #end if
27
28 #if $sec_consensus_variant_calling.prior:
29 --prior "${sec_consensus_variant_calling.prior}"
30 #end if
31 ${sec_consensus_variant_calling.chromosome_X}
32 ${sec_consensus_variant_calling.chromosome_Y}
33
34
35 ## File format section
36 #if str($sec_default.select_output_type) != "__none__":
37 --output-type "${sec_default.select_output_type}"
38 #end if
39 @SEC_DEF_REGIONS@
40 @SEC_DEF_SAMPLES@
41 @SEC_DEF_TARGETS@
42
43
44 ## Input/output section
45 ${sec_input_output.keep_alts}
46 #set values_sec_input_output_format_fields = '","'.join([str($value) for $value in $sec_input_output.format_fields_repeat])
47 #if $values_sec_input_output_format_fields:
48 --format-fields "${values_sec_input_output_format_fields}"
49 #end if
50
51 #if str($sec_input_output.gvcf) != "":
52 --gvcf "${sec_input_output.gvcf}"
53 #end if
54
55 ${sec_input_output.insert_missed}
56 ${sec_input_output.keep_masked_ref}
57
58 #if str($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
64 ## Primary Input/Outputs
65
66 $input_file
67 >
68 $output_file
69 ]]>
70 </command>
71 <inputs>
72 <param name="input_file" label="VCF/BCF Data" type="data" format="vcf,bcf,vcf_bgz,bcf_bgz" />
73 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
74 <param name="select_caller" label="Calling Method" type="select">
75 <option value="consensus">the original calling method (-c, --consensus-caller)</option>
76 <option value="multiallelic">alternative model for multiallelic and rare-variant calling (-m, --multiallelic-caller)</option>
77 </param>
78 <conditional name="constraints" label="Constraints">
79 <param name="constrain_select" label="Constraints" type="select" argument="-C">
80 <option value="__none__" selected="True">No constraints</option>
81 <option value="alleles">call genotypes given alleles (alleles)</option>
82 <option value="trio">call genotypes given the father-mother-child constraint (trio)</option>
83 </param>
84 <when value="__none__" />
85 <when value="alleles" />
86 <when value="trio">
87 <param name="novel_snp" label="Novel Rate: SNPs" type="float" default="1e-8" optional="True" help="mutation rate of SNPs" argument="--novel-rate"/>
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" />
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" />
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"/>
91 </when>
92 </conditional>
93 <param name="prior" label="Prior" type="float" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" argument="--prior" />
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"/>
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"/>
96 </section>
97 <section name="sec_default" expanded="true" title="Default Options">
98 <expand macro="macro_select_output_type" />
99 <expand macro="macro_regions" />
100 <expand macro="macro_samples" />
101 <expand macro="macro_targets" />
102 </section>
103 <section name="sec_input_output" expanded="true" title="Input/output Options">
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"/>
105 <repeat name="format_fields_repeat" title="Format Fields">
106 <param name="format_fields" type="text" label="Format Fields" help="output format fields: e.g. GQ, GP (lowercase allowed)" argument="--format-fields" />
107 </repeat>
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"/>
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"/>
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"/>
111 <param name="skip_variants" label="Skip Variants" type="select" help="Skip indels/SNP sites" argument="--skip-variants">
112 <option value="__none__" selected="True">Don't skip any</option>
113 <option value="indels">Skip indels</option>
114 <option value="snps">Skip snps</option>
115 </param>
116 <param name="variants_only" label="Variants Only" type="boolean" truevalue="--variants-only" falsevalue="" help="output variant sites only" argument="--variants-only"/>
117 </section>
118 </inputs>
119 <outputs>
120 <data name="output_file" format="vcf">
121 <change_format>
122 <when input="sec_file_format|select_output_type" value="b" format="bcf_bgz" />
123 <when input="sec_file_format|select_output_type" value="u" format="bcf" />
124 <when input="sec_file_format|select_output_type" value="z" format="vcf_bgz" />
125 <when input="sec_file_format|select_output_type" value="v" format="vcf" />
126 </change_format>
127 </data>
128 </outputs>
129 <tests>
130 <test>
131 <param name="input_file" value="mpileup.vcf" />
132 <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" />
133 <param name="sec_input_output|variants_only" value="--variants-only" />
134 <param name="sec_file_format|select_output_type" value="v" />
135 <output name="output_file" file="mpileup.1.out" lines_diff="2" ftype="vcf" />
136 </test>
137 <test>
138 <param name="input_file" value="mpileup.vcf" />
139 <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" />
140 <param name="sec_input_output|variants_only" value="--variants-only" />
141 <param name="sec_input_output|gvcf" value="0" />
142 <param name="sec_file_format|select_output_type" value="v" />
143 <output name="output_file" file="mpileup.2.out" lines_diff="2" ftype="vcf" />
144 </test>
145 </tests>
146 <help>
147 <![CDATA[
148 **bcftools call**
149
150 SNP/indel variant calling from VCF/BCF. To be used in conjunction with
151 samtools mpileup. This command replaces the former "bcftools view"
152 caller. Some of the original functionality has been temporarily lost in
153 the process of transition to htslib, but will be added back on popular
154 demand. The original calling model can be invoked with the -c
155 option.
156 ]]>
157 </help>
158 <expand macro="citations" />
159 </tool>