Mercurial > repos > iuc > bcftools_convert_to_vcf

annotate bcftools_convert_to_vcf.xml @ 5:7b50ab23976c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
author iuc
date Thu, 13 Apr 2017 17:41:29 -0400
parents 19167fd970a3
children 367ba501b6eb
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@ to vcf" id="bcftools_@EXECUTABLE@_to_vcf" version="@VERSION@">
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3 <description>Converts other formats to VCF/BCFk</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">convert</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="samtools_requirement"/>
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10 </expand>
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11 <expand macro="version_command" />
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12 <command detect_errors="aggressive"><![CDATA[
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13 @PREPARE_ENV@
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14 #set $input_vcf = None
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15 #if $convert.convert_from == 'gvcf':
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16 #set $input_vcf = 'input.vcf.gz'
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17 #if $convert.input_file.is_of_type('vcf')
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18 bgzip -c '$convert.input_file' > $input_vcf &&
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19 bcftools index $input_vcf &&
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20 #elif $convert.input_file.is_of_type('vcf_bgzip')
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21 ln -s '$convert.input_file' $input_vcf
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22 #elif $convert.input_file.is_of_type('bcf')
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23 #set $input_vcf = 'input.bcf'
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24 ln -s '$convert.input_file' $input_vcf &&
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25 bcftools index $input_vcf &&
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26 #elif $convert.input_file.is_of_type('bcf_bgzip')
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27 ln -s '$convert.input_file' $input_vcf &&
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28 #end if
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29 #end if
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30 #set $section = $convert
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31 @PREPARE_FASTA_REF@
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33 bcftools @EXECUTABLE@
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35 @OUTPUT_TYPE@
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37 #set $section = $convert
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38 #if $convert.convert_from == 'gen_sample':
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39 --gensample2vcf '$convert.input_file,$convert.input_sample'
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40 #elif $convert.convert_from == 'hap_sample':
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41 --hapsample2vcf '$convert.input_file,$convert.input_sample'
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42 #elif $convert.convert_from == 'hap_legend_sample':
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43 --haplegendsample2vcf '$convert.input_file,$convert.input_legend,$convert.input_sample'
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44 #elif $convert.convert_from == 'gvcf':
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45 @FASTA_REF@
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46 --gvcf2vcf $input_vcf
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47 #elif $convert.convert_from == 'tsv':
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48 @FASTA_REF@
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49 @SAMPLES@
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50 @COLUMNS@
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51 --tsv2vcf '$convert.input_file'
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52 #end if
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53 > '$output_file'
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54 ]]>
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55 </command>
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56 <inputs>
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57 <conditional name="convert">
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58 <param name="convert_from" type="select" label="convert from">
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59 <option value="tsv">tsv - TAB-Separated-Value (e.g. 23andMe)</option>
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60 <option value="gvcf">gVCF - GATK Variant Call Format</option>
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61 <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
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62 <option value="hap_sample">haps sample - IMPUTE2 or SHAPEIT</option>
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63 <option value="hap_legend_sample">haps legend sample - IMPUTE2 or SHAPEIT</option>
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64 </param>
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65 <when value="tsv">
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66 <param name="input_file" type="data" format="tabular" label="Tabular Variant Data"
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67 help="Reference sequence and samples are required"/>
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68 <expand macro="macro_fasta_ref" />
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69 <expand macro="macro_samples"/>
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70 <expand macro="macro_columns"/>
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71 </when>
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72 <when value="gvcf">
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73 <param name="input_file" type="data" format="gvcf" label="Genomic VCF (GATK HaplotypeCaller)" />
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74 <expand macro="macro_fasta_ref" />
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75 </when>
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76 <when value="gen_sample">
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77 <param name="input_file" type="data" format="tabular" label="The .gen file" />
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78 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
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79 </when>
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80 <when value="hap_sample">
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81 <param name="input_file" type="data" format="tabular" label="The .hap file" />
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82 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
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83 </when>
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84 <when value="hap_legend_sample">
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85 <param name="input_file" type="data" format="tabular" label="The .hap file" />
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86 <param name="input_legend" type="data" format="tabular" label="The .legend file" />
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87 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
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88 </when>
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89
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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90 </conditional>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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91 <expand macro="macro_select_output_type" />
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92 </inputs>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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93 <outputs>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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94 <expand macro="macro_vcf_output"/>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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95 </outputs>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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96 <tests>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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97 <test>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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98 <param name="convert_from" value="gen_sample" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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99 <param name="input_file" ftype="tabular" value="convert.gs.gt.gen" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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100 <param name="input_sample" ftype="tabular" value="convert.gs.gt.samples" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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101 <param name="output_type" value="v" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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102 <output name="output_file">
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103 <assert_contents>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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104 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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105 <has_text_matching expression="X\t2698560\t.\tG\tA\t.\t.\t.\tGT:GP" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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106 </assert_contents>
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107 </output>
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108 </test>
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109 <test>
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110 <param name="convert_from" value="hap_sample" />
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111 <param name="input_file" ftype="tabular" value="convert.hs.gt.hap" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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112 <param name="input_sample" ftype="tabular" value="convert.hs.gt.samples" />
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113 <param name="output_type" value="v" />
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114 <output name="output_file">
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115 <assert_contents>
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116 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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117 <has_text_matching expression="X\t2698769\t.\tAAG\tA\t.\t.\t.\tGT\t1|0\t1|1\t0|1\t1|0\t1|0\t0|0\t0|0\t0|0\t0|0\t0|0" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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118 </assert_contents>
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119 </output>
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120 </test>
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121 <test>
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122 <param name="convert_from" value="hap_legend_sample" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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123 <param name="input_file" ftype="tabular" value="convert.hls.gt.hap" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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124 <param name="input_legend" ftype="tabular" value="convert.hls.gt.legend" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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125 <param name="input_sample" ftype="tabular" value="convert.hls.gt.samples" />
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126 <param name="output_type" value="v" />
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127 <output name="output_file">
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128 <assert_contents>
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129 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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130 <has_text_matching expression="X\t2698769\t.\tAAG\tA\t.\t.\t.\tGT\t1|0\t1|1\t0|1\t1|0\t1|0\t0|0\t0|0\t0|0\t0|0\t0|0" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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131 </assert_contents>
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132 </output>
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133 </test>
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134 <test>
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135 <param name="convert_from" value="gvcf" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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136 <param name="input_file" ftype="vcf" value="convert.gvcf.vcf" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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137 <param name="fasta_ref" ftype="fasta" value="gvcf.fa" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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138 <param name="output_type" value="v" />
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139 <output name="output_file">
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140 <assert_contents>
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141 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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142 <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tEND=20;BLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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143 </assert_contents>
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144 </output>
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145 </test>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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146 <test>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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147 <param name="convert_from" value="tsv" />
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148 <param name="input_file" ftype="tabular" value="convert.23andme" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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149 <param name="fasta_ref" ftype="fasta" value="23andme.fa" />
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150 <param name="samples" value="SAMPLE1" />
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151 <param name="columns" value="ID,CHROM,POS,AA" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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152 <param name="output_type" value="v" />
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153 <output name="output_file">
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154 <assert_contents>
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155 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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156 <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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157 </assert_contents>
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158 </output>
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159 </test>
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160 </tests>
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161
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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162 <help><![CDATA[
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163 =====================================
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164 bcftools @EXECUTABLE@ plugin
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165 =====================================
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166
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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167 Converts other variant formats to vcf. See man page for file formats details.
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168
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169 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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170
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171 @BCFTOOLS_WIKI@
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172 ]]>
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173 </help>
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174 <expand macro="citations" />
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175 </tool>