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annotate samtools_mpileup.xml @ 4:5872c9894a37 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_mpileup commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:24:45 -0500
parents da0203c3461a
children 483949f5c3b0
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1 <tool id="samtools_mpileup" name="MPileup" version="2.1.1">
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2 <description>call 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>
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10 <![CDATA[
2
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11 #if $reference_source.reference_source_selector == "history":
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12 ln -s "${reference_source.ref_file}" && samtools faidx `basename "${reference_source.ref_file}"` && samtools mpileup
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13 #else:
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14 samtools mpileup
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15 #end if
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16 #if $reference_source.reference_source_selector != "history":
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17 -f "${reference_source.ref_file.fields.path}"
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18 #else:
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19 -f "${reference_source.ref_file}"
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20 #end if
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21 #for $bam in $reference_source.input_bam:
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22 "${bam}"
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23 #end for
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24 #if str( $advanced_options.advanced_options_selector ) == "advanced":
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25 #if str( $advanced_options.filter_by_flags.filter_flags ) == "filter":
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26 #if $advanced_options.filter_by_flags.require_flags:
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27 --rf ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.require_flags).split(',')])}
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28 #end if
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29 #if $advanced_options.filter_by_flags.exclude_flags:
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30 --ff ${sum([int(flag) for flag in str($advanced_options.filter_by_flags.exclude_flags).split(',')])}
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31 #end if
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32 #end if
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33 #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
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34 -l "$pasted_regions"
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35 #elif str( $advanced_options.limit_by_region.limit_by_regions ) == "history"
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36 -l "$advanced_options.limit_by_region.bed_regions"
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37 #end if
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38 #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
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39 -G "$excluded_read_groups"
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40 #elif str( $advanced_options.exclude_read_group.exclude_read_groups ) == "history"
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41 -G "$advanced_options.exclude_read_group.read_groups"
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42 #end if
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43 ${advanced_options.skip_anomalous_read_pairs}
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44 ${advanced_options.disable_probabilistic_realignment}
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45 -C "${advanced_options.coefficient_for_downgrading}"
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46 -d "${advanced_options.max_reads_per_bam}"
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47 ${advanced_options.extended_BAQ_computation}
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48 -q "${advanced_options.minimum_mapping_quality}"
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49 -Q "${advanced_options.minimum_base_quality}"
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50 #if str( $advanced_options.region_string ):
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51 -r "${advanced_options.region_string}"
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52 #end if
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53
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54 #end if
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55 #if str( $genotype_likelihood_computation_type.genotype_likelihood_computation_type_selector ) == 'perform_genotype_likelihood_computation':
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56 ##
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57
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58 ${genotype_likelihood_computation_type.output_format}
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59 ${genotype_likelihood_computation_type.compressed}
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60
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61 #if str( $genotype_likelihood_computation_type.output_tags ) != "None":
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62 --output-tags "${genotype_likelihood_computation_type.output_tags}"
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63 #end if
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64
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65 #if str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'perform_indel_calling':
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66 -o "${genotype_likelihood_computation_type.perform_indel_calling.gap_open_sequencing_error_probability}"
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67 -e "${genotype_likelihood_computation_type.perform_indel_calling.gap_extension_sequencing_error_probability}"
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68 -h "${genotype_likelihood_computation_type.perform_indel_calling.coefficient_for_modeling_homopolymer_errors}"
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69 -L "${genotype_likelihood_computation_type.perform_indel_calling.skip_indel_calling_above_sample_depth}"
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70 -m "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_reads_for_indel_candidates}"
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71 --open-prob "${genotype_likelihood_computation_type.perform_indel_calling.open_seq_error_probability}"
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72 -F "${genotype_likelihood_computation_type.perform_indel_calling.minimum_gapped_read_fraction}"
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73 ${genotype_likelihood_computation_type.perform_indel_calling.gapped_read_per_sample}
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74 #if len( $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ):
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75 -P "${ ",".join( [ str( platform.platform_entry ) for platform in $genotype_likelihood_computation_type.perform_indel_calling.platform_list_repeat ] ) }"
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76 #end if
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77 #elif str( $genotype_likelihood_computation_type.perform_indel_calling.perform_indel_calling_selector ) == 'do_not_perform_indel_calling':
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78 -I
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79 #end if
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80
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81
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82 #else:
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83 ${genotype_likelihood_computation_type.base_position_on_reads}
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84 ${genotype_likelihood_computation_type.output_mapping_quality}
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85 #end if
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86 --output "$output_mpileup" 2> "$output_log"
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87 ]]>
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88 </command>
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89 <inputs>
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90 <conditional name="reference_source">
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91 <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
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92 <option value="cached">Use a built-in genome</option>
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93 <option value="history">Use a genome from the history</option>
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94 </param>
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95 <when value="cached">
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96 <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True">
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97 <validator type="unspecified_build" />
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98 <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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99 </param>
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100 <param label="Using reference genome" name="ref_file" type="select">
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101 <options from_data_table="fasta_indexes" />
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102 </param>
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103 </when>
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104 <when value="history">
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105 <param format="bam" label="BAM file(s)" name="input_bam" type="data" min="1" multiple="True">
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106 <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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107 </param>
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108 <param format="fasta" label="Using reference genome" name="ref_file" type="data" />
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109 </when>
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110 </conditional>
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111 <conditional name="genotype_likelihood_computation_type">
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112 <param label="Genotype Likelihood Computation" name="genotype_likelihood_computation_type_selector" type="select">
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113 <option selected="True" value="perform_genotype_likelihood_computation">Perform genotype likelihood computation (--VCF, --BCF options)</option>
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114 <option value="do_not_perform_genotype_likelihood_computation">Do not perform genotype likelihood computation (output pileup)</option>
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115 </param>
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116 <when value="perform_genotype_likelihood_computation">
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117 <param label="Choose the output format" name="output_format" type="select">
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118 <option value="--VCF">VCF</option>
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119 <option value="--BCF">BCF</option>
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120 </param>
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121 <param checked="False" falsevalue="--uncompressed" label="Compress output" name="compressed" truevalue="" type="boolean" help="--incompressed; default=False"/>
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122 <param name="output_tags" optional="True" type="select" multiple="True" display="checkboxes" label="Optional tags to output" help="--output-tags">
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123 <option value="DP">DP (Number of high-quality bases)</option>
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124 <option value="DPR">DRP (Number of high-quality bases for each observed allele)</option>
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125 <option value="DV">DV (Number of high-quality non-reference bases)</option>
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126 <option value="DP4">DP4 (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases)</option>
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127 <option value="INFO/DPR">INFO/DPR (Number of high-quality bases for each observed allele)</option>
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128 <option value="SP">SP (Phred-scaled strand bias P-value)</option>
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129 </param>
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130 <conditional name="perform_indel_calling">
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131 <param label="Perform INDEL calling" name="perform_indel_calling_selector" type="select">
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132 <option selected="True" value="perform_indel_calling_def">Perform INDEL calling using default options</option>
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133 <option value="perform_indel_calling">Perform INDEL calling and set advanced options</option>
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134 <option value="do_not_perform_indel_calling">Do not perform INDEL calling</option>
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135 </param>
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136 <when value="perform_indel_calling_def" />
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137 <when value="perform_indel_calling">
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138 <param label="Phred-scaled gap open sequencing error probability" name="gap_open_sequencing_error_probability" type="integer" value="40" help="--open-prob; Reducing this value leads to more indel calls; default=40"/>
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139 <param label="Phred-scaled gap extension sequencing error probability" name="gap_extension_sequencing_error_probability" type="integer" value="20" help="--ext-prob; Reducing this value leads to longer indels. default=20"/>
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140 <param label="Coefficient for modeling homopolymer errors." name="coefficient_for_modeling_homopolymer_errors" type="integer" value="100" help="--tandem-qual; default=100"/>
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141 <param label="Skip INDEL calling if the average per-sample depth is above" name="skip_indel_calling_above_sample_depth" type="integer" value="250" help="--max-idepth; default=250"/>
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142 <param label="Minimum gapped reads for indel candidates" name="minimum_gapped_reads_for_indel_candidates" type="integer" value="1" help="--min-ireads; default=1"/>
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143 <param label="Phred-scaled gap open sequencing error probability" name="open_seq_error_probability" type="integer" value="40" help="--open-prob; Reducing this value leads to more indel calls; default=40"/>
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144 <param label="Minimum fraction of gapped reads" name="minimum_gapped_read_fraction" type="float" value="0.002" help="--gap-frac; default=0.002"/>
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145 <param checked="False" falsevalue="" label="Apply --min-ireads and --gap-frac values on a per-sample basis" name="gapped_read_per_sample" truevalue="-p" type="boolean" help="--per-sample-mF; by default both options are applied to reads pooled from all samples"/>
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146 <repeat name="platform_list_repeat" title="Platform for INDEL candidates">
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147 <param label="Platform to use for INDEL candidates" name="platform_entry" type="text" value="" help="It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA"/>
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148 </repeat>
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149 </when>
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150 <when value="do_not_perform_indel_calling" />
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151 </conditional>
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152
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153 </when>
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154 <when value="do_not_perform_genotype_likelihood_computation">
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155 <param checked="False" falsevalue="" label="Output base positions on reads" name="base_position_on_reads" truevalue="-O" type="boolean" help="--output-BP"/>
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156 <param checked="False" falsevalue="" label="Output mapping quality" name="output_mapping_quality" truevalue="-s" type="boolean" help="--output-MQ"/>
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157 </when>
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158 </conditional>
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159 <conditional name="advanced_options">
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160 <param label="Set advanced options" name="advanced_options_selector" type="select">
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161 <option selected="True" value="basic">Basic</option>
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162 <option value="advanced">Advanced</option>
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163 </param>
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164 <when value="advanced">
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165 <conditional name="filter_by_flags">
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166 <param label="Set filter by flags" name="filter_flags" type="select">
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167 <option selected="True" value="nofilter">Do not filter</option>
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168 <option value="filter">Filter by flags to exclude or require</option>
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169 </param>
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170 <when value="filter">
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171 <param display="checkboxes" label="Require" multiple="True" name="require_flags" type="select" help="--incl-flags">
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172 <option value="1">Read is paired</option>
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173 <option value="2">Read is mapped in a proper pair</option>
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174 <option value="4">The read is unmapped</option>
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175 <option value="8">The mate is unmapped</option>
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176 <option value="16">Read strand</option>
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177 <option value="32">Mate strand</option>
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178 <option value="64">Read is the first in a pair</option>
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179 <option value="128">Read is the second in a pair</option>
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180 <option value="256">The alignment or this read is not primary</option>
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181 <option value="512">The read fails platform/vendor quality checks</option>
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182 <option value="1024">The read is a PCR or optical duplicate</option>
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183 </param>
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184 <param display="checkboxes" label="Exclude" multiple="True" name="exclude_flags" type="select" help="--excl-flags">
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185 <option value="1">Read is paired</option>
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186 <option value="2">Read is mapped in a proper pair</option>
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187 <option value="4">The read is unmapped</option>
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188 <option value="8">The mate is unmapped</option>
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189 <option value="16">Read strand</option>
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190 <option value="32">Mate strand</option>
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191 <option value="64">Read is the first in a pair</option>
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192 <option value="128">Read is the second in a pair</option>
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193 <option value="256">The alignment or this read is not primary</option>
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194 <option value="512">The read fails platform/vendor quality checks</option>
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195 <option value="1024">The read is a PCR or optical duplicate</option>
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196 </param>
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197 </when>
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198 <when value="nofilter" />
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199 </conditional>
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200 <conditional name="limit_by_region">
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201 <param label="Select regions to call" name="limit_by_regions" type="select">
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202 <option selected="True" value="no_limit">Do not limit</option>
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203 <option value="history">From an uploaded BED file (--positions)</option>
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204 <option value="paste">Paste a list of regions or BED (--region)</option>
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205 </param>
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206 <when value="history">
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207 <param format="bed" label="BED file" name="bed_regions" type="data" help="--positions">
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208 <validator type="dataset_ok_validator" />
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209 </param>
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210 </when>
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211 <when value="paste">
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212 <param area="true" help="Paste a list of regions in BED format or as a list of chromosomes and positions" label="Regions" name="region_paste" size="10x35" type="text"/>
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213 </when>
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214 <when value="no_limit" />
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215 </conditional>
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216 <conditional name="exclude_read_group">
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217 <param label="Select read groups to exclude" name="exclude_read_groups" type="select" help="--exclude-RG">
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218 <option selected="True" value="no_limit">Do not exclude</option>
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219 <option value="history">From an uploaded text file</option>
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220 <option value="paste">Paste a list of read groups</option>
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221 </param>
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222 <when value="history">
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223 <param format="txt" label="Text file" name="read_groups" type="data">
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224 <validator type="dataset_ok_validator" />
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225 </param>
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226 </when>
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227 <when value="paste">
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228 <param area="true" help="Paste a list of read groups" label="Read groups" name="group_paste" size="10x35" type="text" />
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229 </when>
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230 <when value="no_limit" />
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231 </conditional>
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232 <param checked="False" falsevalue="" label="Disable read-pair overlap detection" name="ignore_overlaps" truevalue="-x" type="boolean" help="--ignore-overlaps"/>
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233 <param checked="False" falsevalue="" label="Do not skip anomalous read pairs in variant calling" name="skip_anomalous_read_pairs" truevalue="-A" type="boolean" help="--count-orphans"/>
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234 <param checked="False" falsevalue="" label="Disable probabilistic realignment for the computation of base alignment quality (BAQ)" name="disable_probabilistic_realignment" truevalue="-B" type="boolean" help="--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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235 <param label="Coefficient for downgrading mapping quality for reads containing excessive mismatches" name="coefficient_for_downgrading" type="integer" value="0" 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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236 <param label="Max reads per BAM" max="1024" min="1" name="max_reads_per_bam" type="integer" value="250" help="--max-depth; default=250"/>
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237 <param checked="False" falsevalue="" label="Redo BAQ computation" name="extended_BAQ_computation" truevalue="-E" type="boolean" help="--redo-BAQ; ignore existing BQ tags"/>
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238 <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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239 <param label="Minimum base quality for a base to be considered" name="minimum_base_quality" type="integer" value="13" help="--min-BQ; default=13"/>
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240 <param label="Only generate pileup in region" name="region_string" type="text" value="" help="--region; If used in conjunction with --positions, then considers the intersection of the two requests. Defaults to all sites" />
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241 </when>
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242 <when value="basic" />
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243 </conditional>
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244 </inputs>
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245 <outputs>
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246 <data format="pileup" label="${tool.name} on ${on_string}" name="output_mpileup">
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247 <change_format>
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248 <when format="bcf" input="genotype_likelihood_computation_type.output_format" value="--BCF" />
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249 <when format="vcf" input="genotype_likelihood_computation_type.output_format" value="--VCF" />
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250 </change_format>
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251 </data>
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252 <data format="txt" label="${tool.name} on ${on_string} (log)" name="output_log" />
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253 </outputs>
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254 <tests>
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255 <test>
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256 <param name="reference_source_selector" value="history" />
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257 <param ftype="fasta" name="ref_file" value="phiX.fasta" />
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258 <param ftype="bam" name="input_bam" value="samtools_mpileup_in_1.bam" />
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259 <param name="genotype_likelihood_computation_type_selector" value="do_not_perform_genotype_likelihood_computation" />
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260 <param name="advanced_options_selector" value="basic" />
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261 <param name="base_position_on_reads" value="true" />
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262 <param name="output_mapping_quality" value="true" />
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263 <output file="samtools_mpileup_out_1.pileup" name="output_mpileup" />
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264 <output file="samtools_mpileup_out_1.log" name="output_log" />
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265 </test>
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266 <test>
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267 <param name="reference_source_selector" value="history" />
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268 <param ftype="fasta" name="ref_file" value="phiX.fasta" />
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269 <param ftype="bam" name="input_bam" value="phiX.bam" />
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270 <param name="genotype_likelihood_computation_type_selector" value="perform_genotype_likelihood_computation" />
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271 <param name="gap_extension_sequencing_error_probability" value="20" />
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272 <param name="coefficient_for_modeling_homopolymer_errors" value="100" />
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273 <param name="perform_indel_calling_selector" value="perform_indel_calling" />
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274 <param name="skip_indel_calling_above_sample_depth" value="250" />
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275 <param name="gap_open_sequencing_error_probability" value="40" />
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276 <param name="platform_list_repeat" value="0" />
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277 <param name="advanced_options_selector" value="basic" />
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278 <param name="genotype_likelihood_computation_type|output_format" value="VCF" />
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279 <output file="samtools_mpileup_out_2.vcf" ftype="vcf" lines_diff="8" name="output_mpileup" />
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280 <output file="samtools_mpileup_out_2.log" name="output_log" />
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281 </test>
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282 </tests>
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283 <help>
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284 <![CDATA[
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285 **What it does**
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286
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287 Report variants 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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288
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289 ------
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290
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291 **Input options**::
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292
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293 -6, --illumina1.3+ quality is in the Illumina-1.3+ encoding
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294 -A, --count-orphans do not discard anomalous read pairs
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295 -b, --bam-list FILE list of input BAM filenames, one per line
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296 -B, --no-BAQ disable BAQ (per-Base Alignment Quality)
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297 -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0]
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298 -d, --max-depth INT max per-BAM depth; avoids excessive memory usage [250]
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299 -E, --redo-BAQ recalculate BAQ on the fly, ignore existing BQs
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300 -f, --fasta-ref FILE faidx indexed reference sequence file
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301 -G, --exclude-RG FILE exclude read groups listed in FILE
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302 -l, --positions FILE skip unlisted positions (chr pos) or regions (BED)
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303 -q, --min-MQ INT skip alignments with mapQ smaller than INT [0]
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304 -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [13]
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305 -r, --region REG region in which pileup is generated
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306 -R, --ignore-RG ignore RG tags (one BAM = one sample)
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307 --rf, --incl-flags STR|INT required flags: skip reads with mask bits unset []
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308 --ff, --excl-flags STR|INT filter flags: skip reads with mask bits set
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309 [UNMAP,SECONDARY,QCFAIL,DUP]
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310 -x, --ignore-overlaps disable read-pair overlap detection
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311
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312 **Output options**::
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313
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314 -o, --output FILE write output to FILE [standard output]
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315 -g, --BCF generate genotype likelihoods in BCF format
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316 -v, --VCF generate genotype likelihoods in VCF format
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317
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318 **Output options for mpileup format** (without -g/-v)::
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319
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320 -O, --output-BP output base positions on reads
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321 -s, --output-MQ output mapping quality
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322
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323 **Output options for genotype likelihoods** (when -g/-v is used)::
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324
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325 -t, --output-tags LIST optional tags to output: DP,DPR,DV,DP4,INFO/DPR,SP []
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326 -u, --uncompressed generate uncompressed VCF/BCF output
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327
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328 **SNP/INDEL genotype likelihoods options** (effective with -g/-v)::
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329
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330 -e, --ext-prob INT Phred-scaled gap extension seq error probability [20]
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331 -F, --gap-frac FLOAT minimum fraction of gapped reads [0.002]
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332 -h, --tandem-qual INT coefficient for homopolymer errors [100]
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333 -I, --skip-indels do not perform indel calling
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334 -L, --max-idepth INT maximum per-sample depth for INDEL calling [250]
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335 -m, --min-ireads INT minimum number gapped reads for indel candidates [1]
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336 -o, --open-prob INT Phred-scaled gap open seq error probability [40]
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337 -p, --per-sample-mF apply -m and -F per-sample for increased sensitivity
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338 -P, --platforms STR comma separated list of platforms for indels [all]
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339
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340 **Notes**: Assuming diploid individuals.
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341 ]]>
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342 </help>
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343 <configfiles>
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344 <configfile name="excluded_read_groups">
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345 <![CDATA[
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346 #set pasted_data = ''
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347 #if str( $advanced_options.advanced_options_selector ) == "advanced":
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348 #if str( $advanced_options.exclude_read_group.exclude_read_groups ) == "paste":
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349 #set pasted_data = '\t'.join( str( $advanced_options.exclude_read_group['read_groups'] ).split() )
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350 #end if
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351 #end if
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352 ${pasted_data}
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353 ]]>
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354 </configfile>
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355 <configfile name="pasted_regions">
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356 <![CDATA[
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357 #set pasted_data = ''
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358 #if str( $advanced_options.advanced_options_selector ) == "advanced":
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359 #if str( $advanced_options.limit_by_region.limit_by_regions ) == "paste":
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360 #set pasted_data = '\t'.join( str( $advanced_options.limit_by_region['region_paste'] ).split() )
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361 #end if
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362 #end if
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363 ${pasted_data}
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364 ]]>
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365 </configfile>
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366 </configfiles>
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367 <expand macro="citations" />
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368 </tool>