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1 <tool id="gatk2_print_reads" name="Print Reads" version="@VERSION@.0">
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2 <description>on BAM files</description>
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3 <macros>
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4 <import>gatk2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command interpreter="python">
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9 gatk2_wrapper.py
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10 --stdout "${output_log}"
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11 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
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12 #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
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13 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
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14 #end if
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15 -p '
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16 @JAR_PATH@
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17 -T "PrintReads"
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18 -o "${output_bam}"
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19 \$GATK2_SITE_OPTIONS
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20
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21 ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
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22 --num_cpu_threads_per_data_thread \${GALAXY_SLOTS:-6}
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23
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24 #if $reference_source.reference_source_selector != "history":
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25 -R "${reference_source.ref_file.fields.path}"
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26 #end if
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27 #if str($input_recal) != 'None':
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28 --BQSR "${input_recal}"
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29 #end if
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30 --disable_bam_indexing
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31 '
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32
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33 #include source=$standard_gatk_options#
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34
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35 ##start analysis specific options
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36 #if $analysis_param_type.analysis_param_type_selector == "advanced":
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37 -p '
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38 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
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39 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
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40 #end if
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41 #if str( $analysis_param_type.default_platform ) != "default":
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42 --default_platform "${analysis_param_type.default_platform}"
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43 #end if
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44 #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
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45 --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
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46 #end if
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47 #if str( $analysis_param_type.force_platform ) != "default":
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48 --force_platform "${analysis_param_type.force_platform}"
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49 #end if
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50 ${analysis_param_type.exception_if_no_tile}
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51 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
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52 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
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53 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}"
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54 #end if
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55 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
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56 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}"
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57 #end if
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58 #end if
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59 ${analysis_param_type.simplify_bam}
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60 --preserve_qscores_less_than "${analysis_param_type.preserve_qscores_less_than}"
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61 --smoothing "${analysis_param_type.smoothing}"
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62 --max_quality_score "${analysis_param_type.max_quality_score}"
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63 --window_size_nqs "${analysis_param_type.window_size_nqs}"
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64 --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
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65 ${analysis_param_type.do_not_write_original_quals}
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66 '
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67 #end if
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68 </command>
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69 <inputs>
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70 <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file"
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71 help="The input covariates table file which enables on-the-fly base quality score recalibration (intended for use with BaseRecalibrator files) (-BQSR,--BQSR)" />
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72 <conditional name="reference_source">
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73 <expand macro="reference_source_selector_param" />
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74 <when value="cached">
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75 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;">
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76 <validator type="unspecified_build" />
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77 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
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78 </param>
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79 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" >
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80 <options from_data_table="gatk2_picard_indexes">
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81 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
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82 </options>
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83 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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84 </param>
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85 </when>
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86 <when value="history">
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87 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" />
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88 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;">
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89 <options>
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90 <filter type="data_meta" key="dbkey" ref="input_bam" />
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91 </options>
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92 </param>
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93 </when>
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94 </conditional>
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95
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96 <expand macro="gatk_param_type_conditional" />
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97
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98 <conditional name="analysis_param_type">
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99 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
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100 <option value="basic" selected="True">Basic</option>
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101 <option value="advanced">Advanced</option>
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102 </param>
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103 <when value="basic">
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104 <!-- Do nothing here -->
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105 </when>
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106 <when value="advanced">
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107 <conditional name="default_read_group_type">
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108 <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group">
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109 <option value="default" selected="True">Don't Set</option>
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110 <option value="set">Set</option>
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111 </param>
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112 <when value="default">
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113 <!-- do nothing here -->
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114 </when>
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115 <when value="set">
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116 <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
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117 </when>
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118 </conditional>
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119 <param name="default_platform" type="select" label="Set default Platform" help="--default_platform">
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120 <option value="default" selected="True">Don't Set</option>
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121 <option value="illumina">illumina</option>
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122 <option value="454">454</option>
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123 <option value="solid">solid</option>
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124 </param>
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125 <conditional name="force_read_group_type">
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126 <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group">
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127 <option value="default" selected="True">Don't Force</option>
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128 <option value="set">Force</option>
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129 </param>
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130 <when value="default">
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131 <!-- do nothing here -->
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132 </when>
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133 <when value="set">
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134 <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
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135 </when>
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136 </conditional>
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137 <param name="force_platform" type="select" label="Force Platform" help="--force_platform">
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138 <option value="default" selected="True">Don't Force</option>
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139 <option value="illumina">illumina</option>
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140 <option value="454">454</option>
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141 <option value="solid">solid</option>
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142 </param>
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143 <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found" help="--exception_if_no_tile"/>
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144 <conditional name="solid_options_type">
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145 <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
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146 <option value="default" selected="True">Don't Set</option>
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147 <option value="set">Set</option>
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148 </param>
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149 <when value="default">
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150 <!-- do nothing here -->
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151 </when>
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152 <when value="set">
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153 <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted" help="-sMode,--solid_recal_mode &lt;solid_recal_mode&gt;">
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154 <option value="default" selected="True">Don't set</option>
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155 <option value="DO_NOTHING">DO_NOTHING</option>
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156 <option value="SET_Q_ZERO">SET_Q_ZERO</option>
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157 <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
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158 <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
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159 </param>
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160 <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls" help="-solid_nocall_strategy,--solid_nocall_strategy &lt;solid_nocall_strategy&gt;">
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161 <option value="default" selected="True">Don't set</option>
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162 <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
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163 <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
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164 <option value="PURGE_READ">PURGE_READ</option>
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165 </param>
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166 </when>
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167 </conditional>
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168 <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
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169 <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="--window_size_nqs"/>
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170 <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &lt;homopolymer_nback&gt;" />
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171 <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated" help="-pQ,--preserve_qscores_less_than &lt;preserve_qscores_less_than&gt;"/>
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172 <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &lt;smoothing&gt;"/>
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173 <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &lt;max_quality_score&gt;"/>
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174 <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/>
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175 </when>
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176 </conditional>
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177 </inputs>
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178 <outputs>
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179 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
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180 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
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181 </outputs>
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182 <tests>
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183 <test>
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184 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
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185 <param name="reference_source_selector" value="history" />
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186 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
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187 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
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188 <param name="gatk_param_type_selector" value="basic" />
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189 <param name="analysis_param_type_selector" value="basic" />
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190 <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" lines_diff="4" />
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191 <output name="output_log" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains" compare="contains" />
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192 </test>
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193 </tests>
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194 <help>
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195 **What it does**
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196
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197 This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal. For each base in each read this walker calculates various user-specified covariates (such as read group, reported quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file with these updated (recalibrated) reads. Note: This walker expects as input the recalibration table file generated previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with CovariateCounterWalker.
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198
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199 For more information on base quality score recalibration using the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_readutils_PrintReads.html>`_.
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200
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201 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_.
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202
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203 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.
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204
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205 ------
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206
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207 **Inputs**
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208
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209 GenomeAnalysisTK: PrintReads accepts an aligned BAM and a recalibration (gatk_report) input files.
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210
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211
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212 **Outputs**
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213
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214 The output is in BAM format.
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215
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216
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217 Go `here <http://www.broadinstitute.org/gatk/guide/topic?name=intro>`_ for details on GATK file formats.
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218
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219 -------
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220
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221 **Settings**::
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222
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223 default_read_group If a read has no read group then default to the provided String.
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224 default_platform If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.
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225 force_read_group If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.
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226 force_platform If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.
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227 window_size_nqs The window size used by MinimumNQSCovariate for its calculation
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228 homopolymer_nback The number of previous bases to look at in HomopolymerCovariate
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229 exception_if_no_tile If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1
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230 solid_recal_mode How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS)
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231 solid_nocall_strategy Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ)
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232 recal_file Filename for the input covariates table recalibration .gatk_report file
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233 out The output BAM file
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234 bam_compression Compression level to use for writing BAM files
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235 disable_bam_indexing Turn off on-the-fly creation of indices for output BAM files.
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236 simplifyBAM If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier
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237 preserve_qscores_less_than Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below < 5, since base callers use these values to indicate random or bad bases
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238 smoothing Number of imaginary counts to add to each bin bin order to smooth out bins with few data points, default=1
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239 max_quality_score The integer value at which to cap the quality scores, default=50
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240 doNotWriteOriginalQuals If true, we will not write the original quality (OQ) tag for each read
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241
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242 @CITATION_SECTION@
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243 </help>
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244 <expand macro="citations" />
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245 </tool>
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