Mercurial > repos > iuc > bcftools_mpileup

annotate bcftools_mpileup.xml @ 13:37757ffb4c5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
author iuc
date Tue, 20 Sep 2022 12:50:07 +0000
parents 31ea13dfe5e6
children bf533509c5b6
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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="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">mpileup</token>
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6 <import>macros.xml</import>
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7 <xml name="bam_flag_options">
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8 <option value="1">Read is paired</option>
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9 <option value="2">Read is mapped in a proper pair</option>
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10 <option value="4">The read is unmapped</option>
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11 <option value="8">The mate is unmapped</option>
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12 <option value="16">Read strand</option>
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13 <option value="32">Mate strand</option>
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14 <option value="64">Read is the first in a pair</option>
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15 <option value="128">Read is the second in a pair</option>
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16 <option value="256">The alignment or this read is not primary</option>
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17 <option value="512">The read fails platform/vendor quality checks</option>
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18 <option value="1024">The read is a PCR or optical duplicate</option>
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19 </xml>
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20 </macros>
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21 <expand macro="bio_tools" />
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22 <expand macro="requirements">
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23 <expand macro="samtools_requirement"/>
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24 </expand>
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25 <expand macro="version_command" />
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26 <command detect_errors="aggressive"><![CDATA[
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27 #import re
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28 #set bam_list = []
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29 #if $input.input_number == 'single':
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30 #set $input_base = $re.sub('\W','_',$input.input_bam.display_name.replace('.bam','').replace('.cram',''))
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31 #set $ext = 'bam'
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32 #set $idx_ext = 'bai'
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33 #if $input.input_bam.ext == 'cram':
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34 #set $ext = 'cram'
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35 #set $idx_ext = 'crai'
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36 #end if
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37 #set $input_name = $input_base + '.' + $ext
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38 #silent $bam_list.append($input_name)
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39 ln -s '${input.input_bam}' ${input_name} &&
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40 #if $input.input_bam.ext == 'bam':
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41 ln -s '${input.input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
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42 #else:
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43 ln -s '${input.input_bam.metadata.cram_index}' ${input_name}.${idx_ext} &&
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44 #end if
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45 #else:
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46 #for $bam_count, $input_bam in enumerate( $input.input_bams ):
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47 #set $input_base = $re.sub('\W','_',$input_bam.display_name.replace('.bam','').replace('.cram',''))
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48 #set $ext = 'bam'
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49 #set $idx_ext = 'bai'
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50 #if $input_bam.ext == 'cram':
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51 #set $ext = 'cram'
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52 #set $idx_ext = 'crai'
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53 #end if
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54 #set $input_name = $input_base + '.' + $ext
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55 #silent $bam_list.append($input_name)
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56 ln -s '${input_bam}' ${input_name} &&
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57 ln -s '${input_bam.metadata.bam_index}' ${input_name}.${idx_ext} &&
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58 #end for
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59 #end if
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60
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61 #set $input_fa_ref = None
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62 #if $reference_source.reference_source_selector == "history":
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63 #set $input_fa_ref = 'ref.fa'
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64 ln -s '${reference_source.ref_file}' $input_fa_ref &&
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65 samtools faidx $input_fa_ref &&
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66 #elif $reference_source.reference_source_selector == "cached":
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67 #set $input_fa_ref = $reference_source.ref_file.fields.path
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68 #end if
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69
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70 #set $section = $sec_restrict
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71 @PREPARE_REGIONS_FILE@
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72 @PREPARE_TARGETS_FILE@
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73
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74 bcftools @EXECUTABLE@
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75
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76 #if $input_fa_ref is not None:
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77 --fasta-ref '$input_fa_ref'
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78 #else:
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79 --non-reference
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80 #end if
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81
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82 ## Indel Calling section
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83 #set $section = $sec_indel
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84 #if $section.perform_indel_calling.perform_indel_calling_selector == 'do_not_perform_indel_calling':
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85 --skip-indels
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86 #elif $section.perform_indel_calling.perform_indel_calling_selector == 'perform_indel_calling':
2
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87 -o "${section.perform_indel_calling.gap_open_sequencing_error_probability}"
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88 -e "${section.perform_indel_calling.gap_extension_sequencing_error_probability}"
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89 -h "${section.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
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90 -L "${section.perform_indel_calling.skip_indel_calling_above_sample_depth}"
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91 -m "${section.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
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92 --open-prob "${section.perform_indel_calling.open_seq_error_probability}"
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93 -F "${section.perform_indel_calling.minimum_gapped_read_fraction}"
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94 ${section.perform_indel_calling.gapped_read_per_sample}
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95 #if len( $section.perform_indel_calling.platform_list_repeat ):
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96 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $section.perform_indel_calling.platform_list_repeat ] ) }"
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97 #end if
0
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98 #end if
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99
13
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100 #if $section.ambig_reads
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101 --ambig-reads $section.ambig_reads
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102 #end if
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103
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104 #if $section.indel_bias
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105 --indel-bias $section.indel_bias
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106 #end if
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107
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108 #if $section.indel_size
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109 --indel-size $section.indel_size
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110 #end if
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111
0
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112 ## Filter section
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113 #set $section = $sec_filtering
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114 #if str( $section.filter_by_flags.filter_flags ) == "filter":
13
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115 #if $section.filter_by_flags.skip_all_set:
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116 --skip-all-set ${sum([int(flag) for flag in str($section.filter_by_flags.skip_all_set).split(',')])}
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117 #end if
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118 #if $section.filter_by_flags.skip_any_set:
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119 --skip-any-set ${sum([int(flag) for flag in str($section.filter_by_flags.skip_any_set).split(',')])}
2
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120 #end if
13
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121 #if $section.filter_by_flags.skip_all_unset:
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122 --skip-all-unset ${sum([int(flag) for flag in str($section.filter_by_flags.skip_all_unset).split(',')])}
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123 #end if
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124 #if $section.filter_by_flags.skip_any_unset:
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125 --skip-any-unset ${sum([int(flag) for flag in str($section.filter_by_flags.skip_any_unset).split(',')])}
2
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126 #end if
0
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127 #end if
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128 -d "${section.max_reads_per_bam}"
12
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129 $section.ignore_overlaps
0
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130 ${section.skip_anomalous_read_pairs}
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131 #if str( $section.quality.quality_settings ) == "adjust":
2
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132 $section.quality.baq
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133 -q "${section.quality.minimum_mapping_quality}"
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134 -Q "${section.quality.minimum_base_quality}"
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135 -C "${section.quality.coefficient_for_downgrading}"
0
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136 #end if
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137 #if str( $section.read_groups.read_groups_selector ) == "ignore_rg":
2
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138 --ignore-RG
0
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139 #elif str( $section.read_groups.read_groups_selector ) == "paste":
2
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140 -G "${section.read_groups.rg_action}${read_groups_file}"
0
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141 #elif str( $section.read_groups.read_groups_selector ) == "history"
2
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142 -G "${section.read_groups.rg_action}${section.read_groups.read_groups}"
0
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143 #end if
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144
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145 #set $section = $sec_output_options
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146 #if $section.output_tags:
2
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147 --annotate "$section.output_tags"
0
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148 #end if
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149 #if $section.gvcf:
2
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150 --gvcf "$section.gvcf"
0
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151 #end if
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152
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153 ## Subset section
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154 #set $section = $sec_subset
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155 @SAMPLES@
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156
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157 ## Restrict section
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158 #set $section = $sec_restrict
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159 @REGIONS@
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160 @TARGETS@
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161 @THREADS@
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162 @OUTPUT_TYPE@
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163
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164 ## Primary Input/Outputs
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165 #echo ' '.join($bam_list)#
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166 > '$output_file'
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167 #if str( $sec_filtering.read_groups.read_groups_selector ) == "paste":
2
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168 && echo 'read-groups:'
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169 && cat ${read_groups_file}
0
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170 #end if
2
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171 ]]></command>
0
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172 <configfiles>
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173 <configfile name="read_groups_file">
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174 <![CDATA[#slurp
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175 #set pasted_data = ''
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176 #set $section = $sec_filtering
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177 #if str( $section.read_groups.read_groups_selector ) == "paste":
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178 #set pasted_data = '\t'.join( str( $section.read_groups.group_paste).split() )
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179 #end if
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180 #slurp
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181 ${pasted_data}
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182 ]]>
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183 </configfile>
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184 </configfiles>
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185 <inputs>
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186
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187 <conditional name="input">
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188 <param name="input_number" type="select" label="Alignment Inputs">
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189 <option value="single">Single BAM/CRAM</option>
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190 <option value="multiple">Multiple BAM/CRAMs</option>
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191 </param>
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192 <when value="single">
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193 <param name="input_bam" type="data" format="bam,cram" label="Input BAM/CRAM" />
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194 </when>
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195 <when value="multiple">
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196 <param name="input_bams" type="data" format="bam,cram" multiple="true" label="Input BAM/CRAMs" />
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197 </when>
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198 </conditional>
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199
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200 <conditional name="reference_source">
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201 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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202 <option value="cached">Locally cached</option>
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203 <option value="history">History</option>
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204 <option value="none">No Reference</option>
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205 </param>
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206 <when value="cached">
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207 <param name="ref_file" type="select" label="Select reference genome">
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208 <options from_data_table="fasta_indexes"/>
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209 </param>
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210 </when>
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211 <when value="history">
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212 <param name="ref_file" type="data" format="fasta" label="Genome Reference" />
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213 </when>
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214 <when value="none"/>
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215 </conditional>
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216
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217 <section name="sec_indel" expanded="false" title="Indel Calling">
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218 <conditional name="perform_indel_calling">
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219 <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling">
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220 <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option>
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221 <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option>
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222 <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option>
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223 </param>
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224 <when value="perform_indel_calling_def" />
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225 <when value="perform_indel_calling">
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226 <param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="--open-prob; Reducing this value leads to more indel calls; default=40"/>
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227 <param name="gap_extension_sequencing_error_probability" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" help="--ext-prob; Reducing this value leads to longer indels. default=20"/>
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228 <param name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" label="Coefficient for modeling homopolymer errors." help="--tandem-qual; default=100"/>
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229 <param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" help="--max-idepth; default=250"/>
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230 <param name="minimum_gapped_reads_for_indel_candidates" type="integer" value="1" label="Minimum gapped reads for indel candidates" help="--min-ireads; default=1"/>
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231 <param name="open_seq_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="--open-prob; Reducing this value leads to more indel calls; default=40"/>
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232 <param name="minimum_gapped_read_fraction" type="float" value="0.002" label="Minimum fraction of gapped reads" help="--gap-frac; default=0.002"/>
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233 <param name="gapped_read_per_sample" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Apply --min-ireads and --gap-frac values on a per-sample basis" help="--per-sample-mF; by default both options are applied to reads pooled from all samples"/>
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234 <repeat name="platform_list_repeat" title="Platform for INDEL candidates">
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235 <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
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236 </repeat>
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237 </when>
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238 <when value="do_not_perform_indel_calling" />
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239 </conditional>
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240 <param argument="--ambig-reads" type="select" optional="true" label="Ambiguous indel reads" help="What to do with ambiguous indel reads that do not span an entire short tandem repeat region: discard ambiguous reads from calling and do not increment high-quality AD depth counters (drop), exclude from calling but increment AD counters proportionally (incAD), exclude from calling and increment the first value of the AD counter (incAD0) ">
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241 <option value="drop">Drop</option>
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242 <option value="incAD">IncAD</option>
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243 <option value="incAD0">IncAD0</option>
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244 </param>
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245 <param argument="--indel-bias" type="float" min="0" value="" optional="true" label="Indel bias" help="Skews the indel scores up or down, trading recall (low false-negative) vs precision (low false-positive) [1.0]. In Bcftools 1.12 and earlier this parameter didn’t exist, but had an implied value of 1.0. If you are planning to do heavy filtering of variants, selecting the best quality ones only (favouring precision over recall), it is advisable to set this lower (such as 0.75) while higher depth samples or where you favour recall rates over precision may work better with a higher value such as 2.0" />
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246 <param argument="--indel-size" type="integer" min="0" value="" optional="true" label="Indel size" help="Indel window size to use when assessing the quality of candidate indels. Note that although the window size approximately corresponds to the maximum indel size considered, it is not an exact threshold. Default: 110" />
0
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247 </section>
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248
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249 <section name="sec_filtering" expanded="false" title="Input Filtering Options">
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250 <param name="max_reads_per_bam" type="integer" value="250" min="1" label="Max reads per BAM" help="--max-depth; default=250"/>
0
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251 <param name="ignore_overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" help="--ignore-overlaps"/>
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252 <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" help="--count-orphans"/>
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253 <conditional name="filter_by_flags">
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254 <param name="filter_flags" type="select" label="Set filter by flags">
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255 <option selected="True" value="nofilter">Do not filter</option>
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256 <option value="filter">Filter by flags to exclude or require</option>
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257 </param>
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258 <when value="filter">
13
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259 <param argument="--skip-all-set" type="select" display="checkboxes" label="Skip reads with all of the FLAG bits set" multiple="True" help="--skip-all-set">
0
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260 <expand macro="bam_flag_options" />
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261 </param>
13
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262 <param argument="--skip-any-set" type="select" display="checkboxes" label="Skip reads with any of the FLAG bits set" multiple="True" help="--skip-any-set">
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263 <expand macro="bam_flag_options" />
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264 </param>
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265 <param argument="--skip-all-unset" type="select" display="checkboxes" label="Skip reads with all of the FLAG bits unset" multiple="True" help="--skip-all-unset">
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266 <expand macro="bam_flag_options" />
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267 </param>
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268 <param argument="--skip-any-unset" type="select" display="checkboxes" label="Skip reads with any of the FLAG bits unset" multiple="True" help="--skip-any-unset">
0
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269 <expand macro="bam_flag_options" />
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270 </param>
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271 </when>
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272 <when value="nofilter" />
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273 </conditional>
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274 <conditional name="quality">
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275 <param label="Quality Options" name="quality_settings" type="select">
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276 <option value="none" selected="True">defaults</option>
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277 <option value="adjust">Set base and mapping quality options</option>
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278 </param>
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279 <when value="adjust">
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280 <param name="baq" type="select" label="per-Base Alignment Quality">
0
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281 <help>
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282 --no-BAQ; BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments.
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283 --redo-BAQ; ignore existing BQ tags
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284 </help>
3
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285 <option value="">Default</option>
0
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286 <option value="--no-BAQ">disable BAQ (per-Base Alignment Quality) (no-BAQ)</option>
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287 <option value="--redo-BAQ">recalculate BAQ on the fly, ignore existing BQs (redo-BAQ)</option>
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288 </param>
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289 <param name="coefficient_for_downgrading" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" help="--adjust-MQ; Given a read with a phred-scaled probability q of being generated from the mapped position, the new mapping quality is about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if enabled, the recommended value for BWA is 50. default=0"/>
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290 <param label="Minimum mapping quality for an alignment to be used" name="minimum_mapping_quality" type="integer" value="0" help="-min-MQ; default=0"/>
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291 <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" help="--min-BQ; default=13"/>
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292 </when>
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293 <when value="none"/>
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294 </conditional>
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295
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296 <conditional name="read_groups">
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297 <param name="read_groups_selector" type="select" label="Select read groups to include or exclude" help="--read-groups">
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298 <option value="no_limit" selected="True">use defaults</option>
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299 <option value="history">From an uploaded text file</option>
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300 <option value="paste">Paste a list of read groups</option>
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301 <option value="ignore_rg">Ignore RG tags. Treat all reads in one alignment file as one sample. </option>
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302 </param>
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303 <when value="history">
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304 <param name="read_groups" format="txt" label="Text file" type="data">
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305 <validator type="dataset_ok_validator" />
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306 </param>
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307 <param name="rg_action" type="select" label="Include or Exclude these Read Groups">
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308 <option value="" selected="true">Include</option>
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309 <option value="^">Exclude</option>
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310 </param>
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311 </when>
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312 <when value="paste">
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313 <param name="group_paste" type="text" size="10x35" area="true" label="Read groups" help="Paste a list of read groups" />
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314 <param name="rg_action" type="select" label="Include or Exclude these Read Groups">
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315 <option value="" selected="true">Include</option>
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316 <option value="^">Exclude</option>
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317 </param>
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318 </when>
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319 <when value="ignore_rg" />
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320 <when value="no_limit" />
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321 </conditional>
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322 </section>
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323
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324 <section name="sec_restrict" expanded="false" title="Restrict to">
4
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325 <expand macro="macro_restrict" />
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326 <expand macro="macro_restrict" type="target" label_type="Target">
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327 <expand macro="macro_invert_targets" />
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328 </expand>
0
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329 </section>
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330 <section name="sec_subset" expanded="false" title="Subset Options">
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331 <expand macro="macro_samples" />
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332 </section>
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333
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334 <section name="sec_output_options" expanded="false" title="Output options">
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335 <expand macro="macro_output_tags">
0
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336 <option value="DP">DP (Number of high-quality bases)</option>
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337 <option value="AD">AD (Allelic depth)</option>
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338 <option value="ADF">ADF (Allelic depth on the forward strand)</option>
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339 <option value="ADR">ADR (Allelic depth on the reverse strand)</option>
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340 <option value="INFO/AD">INFO/AD (Allelic depth)</option>
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341 <option value="INFO/ADF">INFO/ADF (Allelic depth on the forward strand)</option>
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342 <option value="INFO/ADR">INFO/ADR (Allelic depth on the reverse strand)</option>
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343 <option value="SP">SP (Phred-scaled strand bias P-value)</option>
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344 <option value="DV">DV (Number of high-quality non-reference bases)</option>
13
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345 <option value="QS">QS (Allele phred-score quality sum)</option>
0
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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346 <option value="DP4">DP4 (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases)</option>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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347 <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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348 <option value="INFO/DPR">INFO/DPR (Number of high-quality bases for each observed allele)</option>
13
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349 </expand>
0
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350 <param name="gvcf" type="text" value="" label="gVCF blocks of homozygous REF calls">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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351 <help>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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352 output gVCF blocks of homozygous REF calls, with depth (DP) ranges specified by the list of integers. For example, passing 5,15 will group sites into two types of gVCF blocks, the first with minimum per-sample DP from the interval [5,15) and the latter with minimum depth 15 or more. In this example, sites with minimum per-sample depth less than 5 will be printed as separate records, outside of gVCF blocks.
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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353 </help>
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354 <validator type="regex" message="integers separated by commas">^(\d+(,\d+)*)?$</validator>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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355 </param>
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356 </section>
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357
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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358 <expand macro="macro_select_output_type" />
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359
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360 </inputs>
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361 <outputs>
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362 <expand macro="macro_vcf_output" />
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363 </outputs>
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364 <tests>
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365 <test>
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366 <param name="input_number" value="single" />
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367 <param name="input_bam" ftype="bam" value="mpileup.1.bam" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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368 <param name="reference_source_selector" value="history" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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369 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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370 <param name="output_type" value="v" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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371 <output name="output_file">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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372 <assert_contents>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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373 <has_text text="mpileup" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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374 <has_text text="HG00100" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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375 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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376 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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377 </assert_contents>
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378 </output>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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379 </test>
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380 <test>
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381 <param name="input_number" value="single" />
3
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382 <param name="input_bam" ftype="bam" value="mpileup.1.bam" />
4
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383 <param name="reference_source_selector" value="cached" />
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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384 <param name="ref_file" value="mpileup" />
3
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385 <param name="quality_settings" value="adjust" />
4e1d23e5c691 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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386 <param name="output_type" value="v" />
4e1d23e5c691 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
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387 <output name="output_file">
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iuc
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388 <assert_contents>
4e1d23e5c691 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 2
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389 <has_text text="mpileup" />
4e1d23e5c691 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 2
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390 <has_text text="HG00100" />
4e1d23e5c691 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 2
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391 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" />
4e1d23e5c691 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
iuc
parents: 2
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392 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" />
4e1d23e5c691 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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393 </assert_contents>
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394 </output>
4e1d23e5c691 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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395 </test>
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396 <test>
4e1d23e5c691 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 4392ebd727149932e9034f91a21ff520c486052a
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397 <param name="input_number" value="single" />
0
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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398 <param name="input_bam" ftype="cram" value="mpileup.3.cram" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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399 <param name="reference_source_selector" value="history" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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400 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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401 <param name="output_type" value="v" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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402 <output name="output_file">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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403 <assert_contents>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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404 <has_text text="mpileup" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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405 <has_text text="HG00102" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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406 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=5;" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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407 </assert_contents>
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408 </output>
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409 </test>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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410 <test>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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411 <param name="input_number" value="multiple" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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diff changeset
412 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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413 <param name="reference_source_selector" value="history" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
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414 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
4
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diff changeset
415 <section name="sec_restrict">
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416 <conditional name="regions">
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417 <param name="regions_src" value="regions" />
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diff changeset
418 <repeat name="regions">
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419 <param name="chrom" value="17" />
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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420 <param name="start" value="100" />
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421 <param name="stop" value="110" />
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diff changeset
422 </repeat>
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iuc
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diff changeset
423 </conditional>
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
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diff changeset
424 </section>
0
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
425 <param name="output_tags" value="DP,INFO/AD,DV" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
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diff changeset
426 <param name="output_type" value="v" />
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iuc
parents:
diff changeset
427 <output name="output_file">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
428 <assert_contents>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
429 <has_text text="mpileup" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
430 <has_text text="HG00100" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
431 <has_text text="HG00101" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
432 <has_text text="HG00102" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
433 <has_text text="ID=DP," />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
434 <not_has_text text="17\t111" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
435 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=18;AD=17,0;" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
436 </assert_contents>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
437 </output>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
438 </test>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
439 <test>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
440 <param name="input_number" value="multiple" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
441 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
442 <param name="reference_source_selector" value="history" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
443 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
4
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
444 <section name="sec_restrict">
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
445 <conditional name="targets">
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
446 <param name="targets_src" value="targets" />
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
447 <repeat name="targets">
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
448 <param name="chrom" value="17" />
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
449 <param name="start" value="100" />
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
450 <param name="stop" value="104" />
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
451 </repeat>
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
452 </conditional>
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
453 </section>
0
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
454 <param name="output_tags" value="DP,INFO/AD,DV" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
455 <param name="output_type" value="v" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
456 <output name="output_file">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
457 <assert_contents>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
458 <has_text text="mpileup" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
459 <has_text text="HG00100" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
460 <has_text text="HG00101" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
461 <has_text text="HG00102" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
462 <has_text text="ID=DP," />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
463 <not_has_text text="17\t105" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
464 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=18;AD=17,0;" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
465 </assert_contents>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
466 </output>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
467 </test>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
468 <test>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
469 <param name="input_number" value="multiple" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
470 <param name="input_bams" ftype="bam" value="mpileup.1.bam,mpileup.2.bam,mpileup.3.bam" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
471 <param name="reference_source_selector" value="history" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
472 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
4
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
473 <section name="sec_restrict">
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
474 <conditional name="regions">
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
475 <param name="regions_src" value="regions" />
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
476 <repeat name="regions">
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
477 <param name="chrom" value="17" />
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
478 <param name="start" value="1050" />
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
479 <param name="stop" value="1060" />
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
480 </repeat>
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
481 </conditional>
256e65e460b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
iuc
parents: 3
diff changeset
482 </section>
0
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
483 <param name="filter_flags" value="filter" />
13
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
484 <param name="skip_all_set" value="4,16" />
0
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
485 <param name="output_type" value="v" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
486 <output name="output_file">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
487 <assert_contents>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
488 <has_text text="mpileup" />
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
489 <has_text text="HG00100" />
13
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
490 <has_text_matching expression="17\t1050\t.\tA\t" />
0
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
491 </assert_contents>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
492 </output>
13
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
493 <assert_command>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
494 <has_text text="--skip-all-set" />
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
495 </assert_command>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
496 </test>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
497 <!-- Test indel options-->
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
498 <test>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
499 <param name="input_number" value="single" />
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
500 <param name="input_bam" ftype="bam" value="mpileup.1.bam" />
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
501 <param name="reference_source_selector" value="history" />
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
502 <param name="ref_file" ftype="fasta" value="mpileup.ref.fa" />
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
503 <section name="sec_indel">
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
504 <param name="ambig_reads" value="drop"/>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
505 <param name="indel_bias" value="1"/>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
506 <param name="indel_size" value="110"/>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
507 </section>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
508 <param name="output_type" value="v" />
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
509 <output name="output_file">
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
510 <assert_contents>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
511 <has_text text="mpileup" />
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
512 <has_text text="HG00100" />
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
513 <has_text_matching expression="17\t1\t.\tA\t...\t0\t.\tDP=5;" />
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
514 <has_text_matching expression="17\t100\t.\tC\t...\t0\t.\tDP=9;" />
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
515 </assert_contents>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
diff changeset
516 </output>
37757ffb4c5f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49
iuc
parents: 12
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517 <assert_command>
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518 <has_text text="--ambig-reads" />
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519 <has_text text="--indel-bias" />
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520 <has_text text="--indel-size" />
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521 </assert_command>
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522
0
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523 </test>
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524 </tests>
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525 <help><![CDATA[
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526 =====================================
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527 bcftools @EXECUTABLE@
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528 =====================================
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529
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530 Haplotype aware consequence predictor which correctly handles combined variants such as MNPs split over multiple VCF records, SNPs separated by an intron (but adjacent in the spliced transcript) or nearby frame-shifting indels which in combination in fact are not frame-shifting.
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531
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532 The output VCF is annotated with INFO/BCSQ and FORMAT/BCSQ tag (configurable with the -c option). The latter is a bitmask of indexes to INFO/BCSQ, with interleaved haplotypes. See the usage examples below for using the %TBCSQ converter in query for extracting a more human readable form from this bitmask. The contruction of the bitmask limits the number of consequences that can be referenced in the FORMAT/BCSQ tags. By default this is 16, but if more are required, see the --ncsq option.
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533
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534 The program requires on input a VCF/BCF file, the reference genome in fasta format (--fasta-ref) and genomic features in the GFF3 format downloadable from the Ensembl website (--gff-annot), and outputs an annotated VCF/BCF file. Currently, only Ensembl GFF3 files are supported.
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535
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536 By default, the input VCF should be phased. If phase is unknown, or only partially known, the --phase option can be used to indicate how to handle unphased data. Alternatively, haplotype aware calling can be turned off with the --local-csq option.
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537
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538 If conflicting (overlapping) variants within one haplotype are detected, a warning will be emitted and predictions will be based on only the first variant in the analysis.
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539
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540 Symbolic alleles are not supported. They will remain unannotated in the output VCF and are ignored for the prediction analysis.
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541
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542
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543 @REGIONS_HELP@
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544 @TARGETS_HELP@
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545
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546 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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547
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548 @BCFTOOLS_WIKI@
2
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549 ]]></help>
0
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550 <expand macro="citations" />
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551 </tool>