Mercurial > repos > iuc > bcftools_call

annotate 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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a531317a3527 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
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3 <description>SNP/indel variant calling from VCF/BCF</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">call</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="aggressive"><![CDATA[
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11 bcftools @EXECUTABLE@
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12
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13 ## Consensus/variant calling section
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14 #if $sec_consensus_variant_calling.select_caller == "consensus":
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15 --consensus-caller
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16 #else:
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17 --multiallelic-caller
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18 #end if
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20 #if $sec_consensus_variant_calling.constraints.constrain_select == "alleles":
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21 --constrain alleles
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22 #elif $sec_consensus_variant_calling.constraints.constrain_select == "trio":
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23 --constrain trio
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24 --novel-rate ${sec_consensus_variant_calling.constraints.novel_snp},${sec_consensus_variant_calling.constraints.novel_ins},${sec_consensus_variant_calling.constraints.novel_del}
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25 --pval-threshold "${sec_consensus_variant_calling.constraints.pval_threshold}"
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26 #end if
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27
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28 #if $sec_consensus_variant_calling.prior:
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29 --prior "${sec_consensus_variant_calling.prior}"
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30 #end if
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31 ${sec_consensus_variant_calling.chromosome_X}
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32 ${sec_consensus_variant_calling.chromosome_Y}
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33
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34
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35 ## File format section
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36 #if str($sec_default.select_output_type) != "__none__":
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37 --output-type "${sec_default.select_output_type}"
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38 #end if
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39 @SEC_DEF_REGIONS@
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40 @SEC_DEF_SAMPLES@
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41 @SEC_DEF_TARGETS@
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42
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43
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44 ## Input/output section
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45 ${sec_input_output.keep_alts}
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46 #set values_sec_input_output_format_fields = '","'.join([str($value) for $value in $sec_input_output.format_fields_repeat])
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47 #if $values_sec_input_output_format_fields:
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48 --format-fields "${values_sec_input_output_format_fields}"
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49 #end if
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50
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51 #if str($sec_input_output.gvcf) != "":
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52 --gvcf "${sec_input_output.gvcf}"
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53 #end if
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54
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55 ${sec_input_output.insert_missed}
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56 ${sec_input_output.keep_masked_ref}
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57
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58 #if str($sec_input_output.skip_variants) != "__none__":
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59 --skip-variants "${sec_input_output.skip_variants}"
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60 #end if
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61
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62 ${sec_input_output.variants_only}
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63
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64 ## Primary Input/Outputs
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65
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66 $input_file
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67 >
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68 $output_file
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69 ]]>
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70 </command>
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71 <inputs>
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72 <param name="input_file" label="VCF/BCF Data" type="data" format="vcf,bcf,vcf_bgz,bcf_bgz" />
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73 <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
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74 <param name="select_caller" label="Calling Method" type="select">
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75 <option value="consensus">the original calling method (-c, --consensus-caller)</option>
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76 <option value="multiallelic">alternative model for multiallelic and rare-variant calling (-m, --multiallelic-caller)</option>
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77 </param>
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78 <conditional name="constraints" label="Constraints">
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79 <param name="constrain_select" label="Constraints" type="select" argument="-C">
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80 <option value="__none__" selected="True">No constraints</option>
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81 <option value="alleles">call genotypes given alleles (alleles)</option>
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82 <option value="trio">call genotypes given the father-mother-child constraint (trio)</option>
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83 </param>
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84 <when value="__none__" />
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85 <when value="alleles" />
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86 <when value="trio">
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87 <param name="novel_snp" label="Novel Rate: SNPs" type="float" default="1e-8" optional="True" help="mutation rate of SNPs" argument="--novel-rate"/>
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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" />
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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" />
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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"/>
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91 </when>
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92 </conditional>
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93 <param name="prior" label="Prior" type="float" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" argument="--prior" />
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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"/>
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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"/>
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96 </section>
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97 <section name="sec_default" expanded="true" title="Default Options">
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98 <expand macro="macro_select_output_type" />
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99 <expand macro="macro_regions" />
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100 <expand macro="macro_samples" />
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101 <expand macro="macro_targets" />
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102 </section>
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103 <section name="sec_input_output" expanded="true" title="Input/output Options">
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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"/>
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105 <repeat name="format_fields_repeat" title="Format Fields">
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106 <param name="format_fields" type="text" label="Format Fields" help="output format fields: e.g. GQ, GP (lowercase allowed)" argument="--format-fields" />
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107 </repeat>
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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"/>
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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"/>
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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"/>
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111 <param name="skip_variants" label="Skip Variants" type="select" help="Skip indels/SNP sites" argument="--skip-variants">
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112 <option value="__none__" selected="True">Don't skip any</option>
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113 <option value="indels">Skip indels</option>
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114 <option value="snps">Skip snps</option>
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115 </param>
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116 <param name="variants_only" label="Variants Only" type="boolean" truevalue="--variants-only" falsevalue="" help="output variant sites only" argument="--variants-only"/>
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117 </section>
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118 </inputs>
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119 <outputs>
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120 <data name="output_file" format="vcf">
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121 <change_format>
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122 <when input="sec_file_format|select_output_type" value="b" format="bcf_bgz" />
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123 <when input="sec_file_format|select_output_type" value="u" format="bcf" />
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124 <when input="sec_file_format|select_output_type" value="z" format="vcf_bgz" />
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125 <when input="sec_file_format|select_output_type" value="v" format="vcf" />
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126 </change_format>
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127 </data>
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128 </outputs>
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129 <tests>
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130 <test>
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131 <param name="input_file" value="mpileup.vcf" />
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132 <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" />
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133 <param name="sec_input_output|variants_only" value="--variants-only" />
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134 <param name="sec_file_format|select_output_type" value="v" />
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135 <output name="output_file" file="mpileup.1.out" lines_diff="2" ftype="vcf" />
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136 </test>
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137 <test>
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138 <param name="input_file" value="mpileup.vcf" />
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139 <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" />
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140 <param name="sec_input_output|variants_only" value="--variants-only" />
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141 <param name="sec_input_output|gvcf" value="0" />
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142 <param name="sec_file_format|select_output_type" value="v" />
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143 <output name="output_file" file="mpileup.2.out" lines_diff="2" ftype="vcf" />
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144 </test>
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145 </tests>
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146 <help>
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147 <![CDATA[
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148 **bcftools call**
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149
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150 SNP/indel variant calling from VCF/BCF. To be used in conjunction with
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151 samtools mpileup. This command replaces the former "bcftools view"
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152 caller. Some of the original functionality has been temporarily lost in
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153 the process of transition to htslib, but will be added back on popular
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154 demand. The original calling model can be invoked with the -c
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155 option.
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156 ]]>
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157 </help>
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158 <expand macro="citations" />
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159 </tool>