Mercurial > repos > devteam > samtools_mpileup

annotate samtools_mpileup.xml @ 6:483949f5c3b0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:15:58 -0400
parents 5872c9894a37
children edbe9587b15d
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483949f5c3b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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1 <tool id="samtools_mpileup" name="MPileup" version="2.1.3">
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2 <description>multi-way pileup of variants</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command><![CDATA[
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10 #for $bam_count, $input_bam in enumerate( $reference_source.input_bam ):
483949f5c3b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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11 ln -s '${input_bam}' 'localbam_${bam_count}.bam' &&
483949f5c3b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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12 ln -s '${input_bam.metadata.bam_index}' 'localbam_${bam_count}.bam.bai' &&
483949f5c3b0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
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13 #end for
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14
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15 #if $reference_source.reference_source_selector == "history":
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16 ln -s '${reference_source.ref_file}' &&
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17 samtools faidx `basename '${reference_source.ref_file}'` &&
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18 #end if
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20 samtools mpileup
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21 #if $reference_source.reference_source_selector != "history":
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22 -f '${reference_source.ref_file.fields.path}'
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23 #else:
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24 -f '${reference_source.ref_file}'
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25 #end if
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26 #for $bam_count, $input_bam in enumerate( $reference_source.input_bam ):
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27 localbam_${bam_count}.bam
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28 #end for
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29 #if str( $advanced_options.advanced_options_selector ) == "advanced":
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30 #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":
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31 #if $advanced_options.filter_by_flags.require_flags:
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32 --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])}
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33 #end if
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34 #if $advanced_options.filter_by_flags.exclude_flags:
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35 --ff ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.exclude_flags).split(',')])}
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36 #end if
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37 #end if
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38 #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
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39 -l '$pasted_regions'
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40 #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history"
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41 -l '$advanced_options.limit_by_region.bed_regions'
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42 #end if
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43 #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
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44 -G '$excluded_read_groups'
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45 #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"
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46 -G '$advanced_options.exclude_read_group.read_groups'
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47 #end if
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48 ${advanced_options.skip_anomalous_read_pairs}
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49 ${advanced_options.disable_probabilistic_realignment}
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50 -C ${advanced_options.coefficient_for_downgrading}
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51 -d ${advanced_options.max_reads_per_bam}
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52 ${advanced_options.extended_BAQ_computation}
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53 -q ${advanced_options.minimum_mapping_quality}
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54 -Q ${advanced_options.minimum_base_quality}
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55 #if str( $advanced_options.region_string ):
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56 -r '${advanced_options.region_string}'
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57 #end if
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58 #end if
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59 #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation':
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60 ${genotype_likelihood_computation_type.output_format}
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61 ${genotype_likelihood_computation_type.compressed}
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62
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63 #if str( $genotype_likelihood_computation_type.output_tags ) != "None":
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64 --output-tags '${genotype_likelihood_computation_type.output_tags}'
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65 #end if
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66
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67 #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling':
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68 --open-prob ${genotype_likelihood_computation_type.perform_indel_calling.gap_open_sequencing_error_probability}
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69 -e ${genotype_likelihood_computation_type.perform_indel_calling.gap_extension_sequencing_error_probability}
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70 -h ${genotype_likelihood_computation_type.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}
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71 -L ${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}
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72 -m ${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}
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73 -F ${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_read_fraction}
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74 ${genotype_likelihood_computation_type.perform_indel_calling.gapped_read_per_sample}
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75 #if len( $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ):
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76 -P '${ ",".join( str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ) }'
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77 #end if
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78 #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling':
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79 -I
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80 #end if
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81 #else:
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82 ${genotype_likelihood_computation_type.base_position_on_reads}
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83 ${genotype_likelihood_computation_type.output_mapping_quality}
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84 #end if
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85 --output '$output_mpileup'
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86 ]]></command>
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87
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88 <configfiles>
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89 <configfile name="excluded_read_groups"><![CDATA[
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90 #set pasted_data = ''
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91 #if str( $advanced_options.advanced_options_selector ) == "advanced":
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92 #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
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93 #set pasted_data = '\t'.join( str( $advanced_options.exclude_read_group['read_groups'] ).split() )
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94 #end if
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95 #end if
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96 ${pasted_data}
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97 ]]></configfile>
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98 <configfile name="pasted_regions"><![CDATA[
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99 #set pasted_data = ''
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100 #if str( $advanced_options.advanced_options_selector ) == "advanced":
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101 #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
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102 #set pasted_data = '\t'.join( str( $advanced_options.limit_by_region['region_paste'] ).split() )
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103 #end if
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104 #end if
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105 ${pasted_data}
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106 ]]></configfile>
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107 </configfiles>
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108
2
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109 <inputs>
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110 <conditional name="reference_source">
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111 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
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112 <option value="cached">Use a built-in genome</option>
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113 <option value="history">Use a genome from the history</option>
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114 </param>
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115 <when value="cached">
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116 <param name="input_bam" type="data" format="bam" multiple="True" min="1" label="BAM file(s)">
4
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117 <validator type="unspecified_build" />
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118 <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="fasta_indexes" type="dataset_metadata_in_data_table" />
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119 </param>
6
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120 <param name="ref_file" type="select" label="Using reference genome">
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121 <options from_data_table="fasta_indexes" />
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122 </param>
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123 </when>
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124 <when value="history">
6
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125 <param name="input_bam" type="data" format="bam" multiple="True" min="1" label="BAM file(s)">
4
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126 <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
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127 </param>
6
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128 <param name="ref_file" type="data" format="fasta" label="Using reference genome" />
2
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129 </when>
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130 </conditional>
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131 <conditional name="genotype_likelihood_computation_type">
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132 <param name="genotype_likelihood_computation_type_selector" type="select" label="Genotype Likelihood Computation">
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133 <option selected="True" value="perform_genotype_likelihood_computation">Perform genotype likelihood computation (--VCF, --BCF options)</option>
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134 <option value="do_not_perform_genotype_likelihood_computation">Do not perform genotype likelihood computation (output pileup)</option>
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135 </param>
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136 <when value="perform_genotype_likelihood_computation">
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137 <param name="output_format" type="select" label="Choose the output format">
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138 <option value="--VCF">VCF</option>
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139 <option value="--BCF">BCF</option>
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140 </param>
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141 <param name="compressed" argument="--uncompressed" type="boolean" truevalue="" falsevalue="--uncompressed" checked="False" label="Compress output" />
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142 <param name="output_tags" argument="--output-tags" type="select" optional="True" multiple="True" display="checkboxes" label="Optional tags to output">
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143 <option value="DP">DP (Number of high-quality bases)</option>
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144 <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option>
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145 <option value="DV">DV (Number of high-quality non-reference bases)</option>
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146 <option value="DP4">DP4 (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases)</option>
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147 <option value="INFO/DPR">INFO/DPR (Number of high-quality bases for each observed allele)</option>
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148 <option value="SP">SP (Phred-scaled strand bias P-value)</option>
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149 </param>
2
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150 <conditional name="perform_indel_calling">
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151 <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling">
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152 <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option>
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153 <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option>
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154 <option value="do_not_perform_indel_calling">Do not perform INDEL calling (-I)</option>
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155 </param>
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156 <when value="perform_indel_calling_def" />
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157 <when value="perform_indel_calling">
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158 <param name="gap_open_sequencing_error_probability" argument="--open-prob" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" help="Reducing this value leads to more indel calls" />
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159 <param name="gap_extension_sequencing_error_probability" argument="--ext-prob" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" help="Reducing this value leads to longer indels" />
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160 <param name="coefficient_for_modeling_homopolymer_errors" argument="--tandem-qual" type="integer" value="100" label="Coefficient for modeling homopolymer errors" />
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161 <param name="skip_indel_calling_above_sample_depth" argument="--max-idepth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" />
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162 <param name="minimum_gapped_reads_for_indel_candidates" argument="--min-ireads" type="integer" value="1" label="Minimum gapped reads for indel candidates" />
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163 <param name="minimum_gapped_read_fraction" argument="--gap-frac" type="float" value="0.002" label="Minimum fraction of gapped reads" />
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164 <param name="gapped_read_per_sample" argument="--per-sample-mF" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Apply --min-ireads and --gap-frac values on a per-sample basis" help="By default both options are applied to reads pooled from all samples"/>
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165 <repeat name="platform_list_repeat" title="Platform for INDEL candidates" help="--platforms">
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166 <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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167 </repeat>
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168 </when>
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169 <when value="do_not_perform_indel_calling" />
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170 </conditional>
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171
2
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172 </when>
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173 <when value="do_not_perform_genotype_likelihood_computation">
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174 <param name="base_position_on_reads" argument="--output-BP" type="boolean" truevalue="-O" falsevalue="" checked="False" label="Output base positions on reads" />
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175 <param name="output_mapping_quality" argument="--output-MQ" type="boolean" truevalue="-s" falsevalue="" checked="False" label="Output mapping quality" />
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176 </when>
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177 </conditional>
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178 <conditional name="advanced_options">
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179 <param name="advanced_options_selector" type="select" label="Set advanced options">
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180 <option selected="True" value="basic">Basic</option>
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181 <option value="advanced">Advanced</option>
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182 </param>
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183 <when value="basic" />
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184 <when value="advanced">
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185 <conditional name="filter_by_flags">
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186 <param name="filter_flags" type="select" label="Set filter by flags">
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187 <option selected="True" value="nofilter">Do not filter</option>
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188 <option value="filter">Filter by flags to exclude or require</option>
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189 </param>
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190 <when value="filter">
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191 <param name="require_flags" argument="--incl-flags" type="select" multiple="True" display="checkboxes" label="Require">
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192 <option value="1">Read is paired</option>
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193 <option value="2">Read is mapped in a proper pair</option>
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194 <option value="4">The read is unmapped</option>
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195 <option value="8">The mate is unmapped</option>
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196 <option value="16">Read strand</option>
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197 <option value="32">Mate strand</option>
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198 <option value="64">Read is the first in a pair</option>
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199 <option value="128">Read is the second in a pair</option>
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200 <option value="256">The alignment or this read is not primary</option>
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201 <option value="512">The read fails platform/vendor quality checks</option>
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202 <option value="1024">The read is a PCR or optical duplicate</option>
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203 </param>
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204 <param name="exclude_flags" argument="--excl-flags" type="select" multiple="True" display="checkboxes" label="Exclude">
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205 <option value="1">Read is paired</option>
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206 <option value="2">Read is mapped in a proper pair</option>
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207 <option value="4">The read is unmapped</option>
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208 <option value="8">The mate is unmapped</option>
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209 <option value="16">Read strand</option>
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210 <option value="32">Mate strand</option>
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211 <option value="64">Read is the first in a pair</option>
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212 <option value="128">Read is the second in a pair</option>
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213 <option value="256">The alignment or this read is not primary</option>
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214 <option value="512">The read fails platform/vendor quality checks</option>
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215 <option value="1024">The read is a PCR or optical duplicate</option>
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216 </param>
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217 </when>
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218 <when value="nofilter" />
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219 </conditional>
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220 <conditional name="limit_by_region">
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221 <param name="limit_by_regions" argument="--positions" type="select" label="Select regions to call">
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222 <option selected="True" value="no_limit">Do not limit</option>
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223 <option value="history">From a BED file</option>
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224 <option value="paste">Paste a list of regions or BED</option>
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225 </param>
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226 <when value="history">
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227 <param name="bed_regions" type="data" format="bed" label="BED file">
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228 <validator type="dataset_ok_validator" />
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229 </param>
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230 </when>
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231 <when value="paste">
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232 <param name="region_paste" type="text" area="true" size="10x35" label="Regions" help="Paste a list of regions in BED format or as a list of chromosomes and positions" />
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233 </when>
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234 <when value="no_limit" />
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235 </conditional>
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236 <conditional name="exclude_read_group">
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237 <param name="exclude_read_groups" argument="--exclude-RG" type="select" label="Select read groups to exclude">
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238 <option selected="True" value="no_limit">Do not exclude</option>
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239 <option value="history">From a text file</option>
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240 <option value="paste">Paste a list of read groups</option>
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241 </param>
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242 <when value="history">
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243 <param name="read_groups" type="data" format="txt" label="Text file">
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244 <validator type="dataset_ok_validator" />
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245 </param>
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246 </when>
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247 <when value="paste">
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248 <param name="group_paste" type="text" area="true" size="10x35" label="Read groups" help="Paste a list of read groups" />
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249 </when>
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250 <when value="no_limit" />
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251 </conditional>
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252 <param name="ignore_overlaps" argument="--ignore-overlaps" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Disable read-pair overlap detection" />
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253 <param name="skip_anomalous_read_pairs" argument="--count-orphans" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" />
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254 <param name="disable_probabilistic_realignment" argument="--no-BAQ" type="boolean" truevalue="-B" falsevalue="" checked="False" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" help="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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255 <param name="coefficient_for_downgrading" argument="--adjust-MQ" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" help="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" />
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256 <param name="max_reads_per_bam" argument="--max-depth" type="integer" max="1024" min="1" value="250" label="Max reads per BAM" />
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257 <param name="extended_BAQ_computation" argument="--redo-BAQ" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Redo BAQ computation" help="Ignore existing BQ tags" />
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258 <param name="minimum_mapping_quality" argument="--min-MQ" type="integer" value="0" label="Minimum mapping quality for an alignment to be used" />
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259 <param name="minimum_base_quality" argument="--min-BQ" type="integer" value="13" label="Minimum base quality for a base to be considered" />
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260 <param name="region_string" argument="--region" type="text" value="" label="Only generate pileup in region" help="If used in conjunction with --positions, then considers the intersection of the two requests. Defaults to all sites" />
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261 </when>
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262 </conditional>
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263 </inputs>
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264 <outputs>
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265 <data name="output_mpileup" format="pileup" label="${tool.name} on ${on_string}">
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266 <change_format>
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267 <when format="bcf" input="genotype_likelihood_computation_type.output_format" value="--BCF" />
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268 <when format="vcf" input="genotype_likelihood_computation_type.output_format" value="--VCF" />
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269 </change_format>
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270 </data>
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271 </outputs>
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272 <tests>
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273 <test>
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274 <param name="reference_source_selector" value="history" />
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275 <param name="ref_file" ftype="fasta" value="phiX.fasta" />
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276 <param name="input_bam" ftype="bam" value="samtools_mpileup_in_1.bam" />
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277 <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" />
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278 <param name="advanced_options_selector" value="basic" />
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279 <param name="base_position_on_reads" value="true" />
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280 <param name="output_mapping_quality" value="true" />
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281 <output name="output_mpileup" file="samtools_mpileup_out_1.pileup" />
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282 </test>
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283 <test>
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284 <param name="reference_source_selector" value="history" />
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285 <param name="ref_file" ftype="fasta" value="phiX.fasta" />
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286 <param name="input_bam" ftype="bam" value="phiX.bam" />
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287 <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" />
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288 <param name="gap_extension_sequencing_error_probability" value="20" />
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289 <param name="coefficient_for_modeling_homopolymer_errors" value="100" />
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290 <param name="perform_indel_calling_selector" value="perform_indel_calling" />
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291 <param name="skip_indel_calling_above_sample_depth" value="250" />
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292 <param name="gap_open_sequencing_error_probability" value="40" />
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293 <param name="platform_list_repeat" value="0" />
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294 <param name="advanced_options_selector" value="basic" />
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295 <param name="genotype_likelihood_computation_type|output_format" value="VCF" />
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296 <output name="output_mpileup" file="samtools_mpileup_out_2.vcf" ftype="vcf" lines_diff="8" />
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297 </test>
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298 <test>
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299 <param name="reference_source_selector" value="history" />
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300 <param name="ref_file" ftype="fasta" value="phiX.fasta" />
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301 <param name="input_bam" ftype="bam" value="samtools_mpileup_in_1.bam" />
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302 <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" />
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303 <param name="advanced_options_selector" value="advanced" />
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304 <param name="minimum_base_quality" value="0" /><!-- most reads have ultra low quality resuling in empty columns -->
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305 <param name="base_position_on_reads" value="true" />
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306 <param name="output_mapping_quality" value="true" />
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307 <output name="output_mpileup" file="samtools_mpileup_out_3.pileup" />
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308 </test>
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309 </tests>
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310 <help><![CDATA[
0
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311 **What it does**
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312
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313 Report variants for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines.
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314 If sample identifiers are absent, each input file is regarded as one sample.
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315
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316 **Notes**: Assuming diploid individuals.
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317 ]]></help>
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318 <expand macro="citations" />
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319 </tool>