Mercurial > repos > iuc > bcftools_convert_to_vcf

annotate bcftools_convert_to_vcf.xml @ 8:843e008b15fd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 13:11:03 -0400
parents 367ba501b6eb
children 8bb5efd7a3dd
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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="@TOOL_VERSION@+galaxy1">
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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 #if $convert.convert_from == 'gvcf' or $convert.convert_from == 'tsv':
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31 #set $section = $convert.reference_source
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32 @PREPARE_FASTA_REF@
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33 #end if
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35 bcftools @EXECUTABLE@
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37 @OUTPUT_TYPE@
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39 #if $convert.convert_from == 'gen_sample':
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40 --gensample2vcf '$convert.input_file,$convert.input_sample'
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41 #elif $convert.convert_from == 'hap_sample':
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42 --hapsample2vcf '$convert.input_file,$convert.input_sample'
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43 #elif $convert.convert_from == 'hap_legend_sample':
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44 --haplegendsample2vcf '$convert.input_file,$convert.input_legend,$convert.input_sample'
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45 #elif $convert.convert_from == 'gvcf':
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46 @FASTA_REF@
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47 --gvcf2vcf $input_vcf
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48 #elif $convert.convert_from == 'tsv':
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49 @FASTA_REF@
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50 #set $section = $convert
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51 @SAMPLES@
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52 @COLUMNS@
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53 --tsv2vcf '$convert.input_file'
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54 #end if
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55 > '$output_file'
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56 ]]>
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57 </command>
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58 <inputs>
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59 <conditional name="convert">
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60 <param name="convert_from" type="select" label="convert from">
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61 <option value="tsv">tsv - TAB-Separated-Value (e.g. 23andMe)</option>
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62 <option value="gvcf">gVCF - GATK Variant Call Format</option>
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63 <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
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64 <option value="hap_sample">haps sample - IMPUTE2 or SHAPEIT</option>
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65 <option value="hap_legend_sample">haps legend sample - IMPUTE2 or SHAPEIT</option>
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66 </param>
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67 <when value="tsv">
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68 <param name="input_file" type="data" format="tabular" label="Tabular Variant Data"
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69 help="Reference sequence and samples are required"/>
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70 <expand macro="macro_fasta_ref" />
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71 <expand macro="macro_samples"/>
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72 <expand macro="macro_columns"/>
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73 </when>
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74 <when value="gvcf">
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75 <param name="input_file" type="data" format="vcf" label="Genomic VCF (GATK HaplotypeCaller)" />
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76 <expand macro="macro_fasta_ref" />
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77 </when>
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78 <when value="gen_sample">
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79 <param name="input_file" type="data" format="tabular" label="The .gen file" />
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80 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
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81 </when>
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82 <when value="hap_sample">
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83 <param name="input_file" type="data" format="tabular" label="The .hap file" />
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84 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
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85 </when>
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86 <when value="hap_legend_sample">
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87 <param name="input_file" type="data" format="tabular" label="The .hap file" />
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88 <param name="input_legend" type="data" format="tabular" label="The .legend file" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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89 <param name="input_sample" type="data" format="tabular" label="The .samples file" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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90 </when>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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91
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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92 </conditional>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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93 <expand macro="macro_select_output_type" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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94 </inputs>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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95 <outputs>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
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96 <expand macro="macro_vcf_output"/>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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97 </outputs>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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98 <tests>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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99 <test>
8
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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100 <conditional name="convert">
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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101 <param name="convert_from" value="gen_sample" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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102 <param name="input_file" ftype="tabular" value="convert.gs.gt.gen" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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103 <param name="input_sample" ftype="tabular" value="convert.gs.gt.samples" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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104 </conditional>
0
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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105 <param name="output_type" value="v" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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106 <output name="output_file">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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107 <assert_contents>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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108 <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
iuc
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109 <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
iuc
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110 </assert_contents>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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111 </output>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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112 </test>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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113 <test>
8
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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114 <conditional name="convert">
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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115 <param name="convert_from" value="hap_sample" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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116 <param name="input_file" ftype="tabular" value="convert.hs.gt.hap" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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117 <param name="input_sample" ftype="tabular" value="convert.hs.gt.samples" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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118 </conditional>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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119 <param name="output_type" value="v" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
120 <output name="output_file">
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
121 <assert_contents>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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parents: 7
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122 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tNA00001\tNA00002\tNA00003\tNA00004\tNA00005\tNA00006\tNA00007\tNA00008\tNA00009\tNA00010" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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123 <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" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
124 </assert_contents>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
125 </output>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
126 </test>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
127 <test>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
128 <conditional name="convert">
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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129 <param name="convert_from" value="hap_legend_sample" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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130 <param name="input_file" ftype="tabular" value="convert.hls.gt.hap" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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131 <param name="input_legend" ftype="tabular" value="convert.hls.gt.legend" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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132 <param name="input_sample" ftype="tabular" value="convert.hls.gt.samples" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
133 </conditional>
0
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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134 <param name="output_type" value="v" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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135 <output name="output_file">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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136 <assert_contents>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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137 <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
iuc
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138 <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
iuc
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139 </assert_contents>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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140 </output>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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141 </test>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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142 <test>
8
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
143 <conditional name="convert">
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
144 <param name="convert_from" value="gvcf" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
145 <param name="input_file" ftype="vcf" value="convert.gvcf.vcf" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
146 <expand macro="test_using_reference" ref="gvcf.fa" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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147 </conditional>
0
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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148 <param name="output_type" value="v" />
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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149 <output name="output_file">
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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150 <assert_contents>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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151 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" />
7
367ba501b6eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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parents: 5
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152 <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" />
0
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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153 </assert_contents>
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154 </output>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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155 </test>
b068ef999550 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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156 <test>
8
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
157 <conditional name="convert">
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158 <param name="convert_from" value="gvcf" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
159 <param name="input_file" ftype="vcf" dbkey="?" value="convert.gvcf.vcf" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
160 <expand macro="test_using_reference" select_from="cached" ref="gvcf" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
161 </conditional>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
162 <param name="output_type" value="v" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
163 <output name="output_file">
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
164 <assert_contents>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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parents: 7
diff changeset
165 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE99" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
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166 <has_text_matching expression="22\t10\t.\tC\t.\t0\tLowGQX\tBLOCKAVG_min30p3a\tGT:GQX:DP:DPF\t0/0:5:2:0" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
167 </assert_contents>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
168 </output>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
169 </test>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
170 <test>
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
171 <conditional name="convert">
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iuc
parents: 7
diff changeset
172 <param name="convert_from" value="tsv" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
173 <param name="input_file" ftype="tabular" value="convert.23andme" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 7
diff changeset
174 <expand macro="test_using_reference" ref="23andme.fa" />
843e008b15fd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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175 <param name="samples" value="SAMPLE1" />
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176 <param name="columns" value="ID,CHROM,POS,AA" />
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177 </conditional>
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178 <param name="output_type" value="v" />
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179 <output name="output_file">
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180 <assert_contents>
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181 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" />
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182 <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" />
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183 </assert_contents>
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184 </output>
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185 </test>
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186 <test>
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187 <conditional name="convert">
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188 <param name="convert_from" value="tsv" />
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189 <param name="input_file" ftype="tabular" dbkey="?" value="convert.23andme" />
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190 <expand macro="test_using_reference" select_from="cached" ref="23andme" />
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191 <param name="samples" value="SAMPLE1" />
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192 <param name="columns" value="ID,CHROM,POS,AA" />
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193 </conditional>
0
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194 <param name="output_type" value="v" />
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195 <output name="output_file">
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196 <assert_contents>
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197 <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tSAMPLE1" />
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198 <has_text_matching expression="1\t10\trs002\tG\tA\t.\t.\t.\tGT\t1/0" />
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199 </assert_contents>
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200 </output>
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201 </test>
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202 </tests>
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203
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204 <help><![CDATA[
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205 =====================================
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206 bcftools @EXECUTABLE@ plugin
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207 =====================================
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208
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209 Converts other variant formats to vcf. See man page for file formats details.
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210
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211 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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212
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213 @BCFTOOLS_WIKI@
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214 ]]>
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215 </help>
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216 <expand macro="citations" />
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217 </tool>