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1 <tool id="samtools_mpileup" name="MPileup" version="0.0.1">
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2 <description>SNP and indel caller</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.18">samtools</requirement>
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5 </requirements>
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6 <command interpreter="python">samtools_wrapper.py
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7 -p 'samtools mpileup'
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8 --stdout "${output_log}"
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9 #if $reference_source.reference_source_selector != "history":
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10 -p '-f "${reference_source.ref_file.fields.path}"'
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11 #else:
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12 -d "-f" "${reference_source.ref_file}" "fa" "reference_input"
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13 #end if
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14 #for $i, $input_bam in enumerate( $reference_source.input_bams ):
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15 -d " " "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "bam_input_${i}"
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16 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "bam_input_${i}" ##hardcode galaxy ext type as bam_index
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17 #end for
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18 -p '
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19 #if str( $advanced_options.advanced_options_selector ) == "advanced":
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20 ${advanced_options.skip_anomalous_read_pairs}
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21 ${advanced_options.disable_probabilistic_realignment}
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22 -C "${advanced_options.coefficient_for_downgrading}"
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23 -d "${advanced_options.max_reads_per_bam}"
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24 ${advanced_options.extended_BAQ_computation}
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25 #if str( $advanced_options.position_list ) != 'None':
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26 -l "${advanced_options.position_list}"
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27 #end if
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28 -q "${advanced_options.minimum_mapping_quality}"
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29 -Q "${advanced_options.minimum_base_quality}"
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30 #if str( $advanced_options.region_string ):
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31 -r "${advanced_options.region_string}"
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32 #end if
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33 ${advanced_options.output_per_sample_read_depth}
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34 ${advanced_options.output_per_sample_strand_bias_p_value}
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35 #end if
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36 #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation':
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37 ##-g or -u
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38 -g
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39 -e "${genotype_likelihood_computation_type.gap_extension_sequencing_error_probability}"
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40 -h "${genotype_likelihood_computation_type.coefficient_for_modeling_homopolymer_errors}"
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41 #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling':
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42 -L "${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}"
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43 #else:
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44 -I
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45 #end if
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46 -o "${genotype_likelihood_computation_type.gap_open_sequencing_error_probability}"
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47 #if len( $genotype_likelihood_computation_type.platform_list_repeat ):
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48 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.platform_list_repeat ] ) }"
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49 #end if
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50 #end if
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51 > "${output_mpileup}"
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52 '
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53 </command>
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54 <inputs>
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55 <conditional name="reference_source">
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56 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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57 <option value="cached">Locally cached</option>
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58 <option value="history">History</option>
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59 </param>
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60 <when value="cached">
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61 <repeat name="input_bams" title="BAM file" min="1">
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62 <param name="input_bam" type="data" format="bam" label="BAM file">
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63 <validator type="unspecified_build" />
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64 <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="value" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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65 </param>
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66 </repeat>
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67 <param name="ref_file" type="select" label="Using reference genome">
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68 <options from_data_table="sam_fa_indexes">
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69 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...-->
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70 </options>
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71 </param>
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72 </when>
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73 <when value="history"> <!-- FIX ME!!!! -->
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74 <repeat name="input_bams" title="BAM file" min="1">
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75 <param name="input_bam" type="data" format="bam" label="BAM file" >
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76 <validator type="metadata" check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue."/>
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77 </param>
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78 </repeat>
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79 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
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80 </when>
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81 </conditional>
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82
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83
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84 <conditional name="genotype_likelihood_computation_type">
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85 <param name="genotype_likelihood_computation_type_selector" type="select" label="Genotype Likelihood Computation">
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86 <option value="perform_genotype_likelihood_computation">Perform genotype likelihood computation</option>
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87 <option value="do_not_perform_genotype_likelihood_computation" selected="True">Do not perform genotype likelihood computation</option>
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88 </param>
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89 <when value="perform_genotype_likelihood_computation">
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90 <param name="gap_extension_sequencing_error_probability" type="integer" value="20" label="Phred-scaled gap extension sequencing error probability" />
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91 <param name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" label="Coefficient for modeling homopolymer errors." />
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92 <conditional name="perform_indel_calling">
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93 <param name="perform_indel_calling_selector" type="select" label="Perform INDEL calling">
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94 <option value="perform_indel_calling" selected="True">Perform INDEL calling</option>
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95 <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option>
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96 </param>
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97 <when value="perform_indel_calling">
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98 <param name="skip_indel_calling_above_sample_depth" type="integer" value="250" label="Skip INDEL calling if the average per-sample depth is above" />
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99 </when>
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100 <when value="do_not_perform_indel_calling" />
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101 </conditional>
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102 <param name="gap_open_sequencing_error_probability" type="integer" value="40" label="Phred-scaled gap open sequencing error probability" />
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103 <repeat name="platform_list_repeat" title="Platform for INDEL candidates">
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104 <param name="platform_entry" type="text" value="" label="Platform to use for INDEL candidates" />
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105 </repeat>
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106 </when>
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107 <when value="do_not_perform_genotype_likelihood_computation">
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108 <!-- Do nothing here -->
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109 </when>
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110 </conditional>
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111 <conditional name="advanced_options">
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112 <param name="advanced_options_selector" type="select" label="Set advanced options">
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113 <option value="basic" selected="True">Basic</option>
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114 <option value="advanced">Advanced</option>
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115 </param>
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116 <when value="advanced">
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117 <param name="skip_anomalous_read_pairs" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Do not skip anomalous read pairs in variant calling" />
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118 <param name="disable_probabilistic_realignment" type="boolean" truevalue="-B" falsevalue="" checked="False" label=" Disable probabilistic realignment for the computation of base alignment quality (BAQ)" />
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119 <param name="coefficient_for_downgrading" type="integer" value="0" label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" />
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120 <param name="max_reads_per_bam" type="integer" value="250" label="Max reads per BAM" />
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121 <param name="extended_BAQ_computation" type="boolean" truevalue="-E" falsevalue="" checked="False" label="Extended BAQ computation" />
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122 <param name="position_list" type="data" format="bed" label="List of regions or sites on which to operate" optional="True" />
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123 <param name="minimum_mapping_quality" type="integer" value="0" label="Minimum mapping quality for an alignment to be used" />
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124 <param name="minimum_base_quality" type="integer" value="13" label="Minimum base quality for a base to be considered" />
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125 <param name="region_string" type="text" value="" label="Only generate pileup in region" />
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126 <param name="output_per_sample_read_depth" type="boolean" truevalue="-D" falsevalue="" checked="False" label="Output per-sample read depth" />
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127 <param name="output_per_sample_strand_bias_p_value" type="boolean" truevalue="-S" falsevalue="" checked="False" label="Output per-sample Phred-scaled strand bias P-value" />
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128 </when>
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129 <when value="basic" />
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130 </conditional>
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131 </inputs>
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132 <outputs>
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133 <data format="pileup" name="output_mpileup" label="${tool.name} on ${on_string}">
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134 <change_format>
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135 <when input="genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" format="bcf" />
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136 </change_format>
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137 </data>
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138 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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139 </outputs>
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140 <tests>
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141 <test>
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142 <param name="reference_source_selector" value="history" />
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143 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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144 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
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145 <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" />
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146 <param name="advanced_options_selector" value="basic" />
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147 <output name="output_mpileup" file="samtools/mpileup/samtools_mpileup_out_1.pileup" />
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148 <output name="output_log" file="samtools/mpileup/samtools_mpileup_out_1.log" />
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149 </test>
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150 <test>
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151 <param name="reference_source_selector" value="history" />
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152 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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153 <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
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154 <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" />
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155 <param name="gap_extension_sequencing_error_probability" value="20" />
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156 <param name="coefficient_for_modeling_homopolymer_errors" value="100" />
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157 <param name="perform_indel_calling_selector" value="perform_indel_calling" />
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158 <param name="skip_indel_calling_above_sample_depth" value="250" />
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159 <param name="gap_open_sequencing_error_probability" value="40" />
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160 <param name="platform_list_repeat" value="0" />
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161 <param name="advanced_options_selector" value="basic" />
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162 <output name="output_mpileup" file="samtools/mpileup/samtools_mpileup_out_2.bcf" />
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163 <output name="output_log" file="samtools/mpileup/samtools_mpileup_out_1.log" />
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164 </test>
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165 </tests>
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166 <help>
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167 **What it does**
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168
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169 Generate BCF or pileup for one or multiple BAM files. Alignment records are grouped by sample identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample.
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170
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171 ------
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172
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173 **Settings**::
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174
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175 Input Options:
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176 -6 Assume the quality is in the Illumina 1.3+ encoding.
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177 -A Do not skip anomalous read pairs in variant calling.
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178 -B Disable probabilistic realignment for the computation of base alignment quality (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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179 -b FILE List of input BAM files, one file per line [null]
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180 -C INT Coefficient for downgrading mapping quality for reads containing excessive mismatches. 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. [0]
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181 -d INT At a position, read maximally INT reads per input BAM. [250]
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182 -E Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt specificity a little bit.
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183 -f FILE The faidx-indexed reference file in the FASTA format. The file can be optionally compressed by razip. [null]
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184 -l FILE BED or position list file containing a list of regions or sites where pileup or BCF should be generated [null]
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185 -q INT Minimum mapping quality for an alignment to be used [0]
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186 -Q INT Minimum base quality for a base to be considered [13]
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187 -r STR Only generate pileup in region STR [all sites]
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188 Output Options:
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189
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190 -D Output per-sample read depth
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191 -g Compute genotype likelihoods and output them in the binary call format (BCF).
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192 -S Output per-sample Phred-scaled strand bias P-value
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193 -u Similar to -g except that the output is uncompressed BCF, which is preferred for piping.
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194
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195 Options for Genotype Likelihood Computation (for -g or -u):
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196
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197 -e INT Phred-scaled gap extension sequencing error probability. Reducing INT leads to longer indels. [20]
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198 -h INT Coefficient for modeling homopolymer errors. Given an l-long homopolymer run, the sequencing error of an indel of size s is modeled as INT*s/l. [100]
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199 -I Do not perform INDEL calling
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200 -L INT Skip INDEL calling if the average per-sample depth is above INT. [250]
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201 -o INT Phred-scaled gap open sequencing error probability. Reducing INT leads to more indel calls. [40]
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202 -P STR Comma dilimited list of platforms (determined by @RG-PL) from which indel candidates are obtained. It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA. [all]
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203
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204 ------
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205
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206 **Citation**
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207
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208 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
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209
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210 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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211
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212 </help>
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213 </tool>
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