/tools/gatk/table_recalibration.xml
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1<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.5"> 2 <description>on BAM files</description> 3 <requirements> 4 <requirement type="package" version="1.4">gatk</requirement> 5 <requirement type="package">samtools</requirement> 6 </requirements> 7 <macros> 8 <import>gatk_macros.xml</import> 9 </macros> 10 <command interpreter="python">gatk_wrapper.py 11 --max_jvm_heap_fraction "1" 12 --stdout "${output_log}" 13 -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input" 14 #if str( $reference_source.input_bam.metadata.bam_index ) != "None": 15 -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index 16 #end if 17 -p 'java 18 -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" 19 -T "TableRecalibration" 20 -o "${output_bam}" 21 -et "NO_ET" ##ET no phone home 22 ##--num_threads 4 ##hard coded, for now 23 ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout 24 #if $reference_source.reference_source_selector != "history": 25 -R "${reference_source.ref_file.fields.path}" 26 #end if 27 --recal_file "${input_recal}" 28 --disable_bam_indexing 29 ' 30 #include source=$standard_gatk_options# 31 32 ##start analysis specific options 33 #if $analysis_param_type.analysis_param_type_selector == "advanced": 34 -p ' 35 #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set": 36 --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}" 37 #end if 38 #if str( $analysis_param_type.default_platform ) != "default": 39 --default_platform "${analysis_param_type.default_platform}" 40 #end if 41 #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set": 42 --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}" 43 #end if 44 #if str( $analysis_param_type.force_platform ) != "default": 45 --force_platform "${analysis_param_type.force_platform}" 46 #end if 47 ${analysis_param_type.exception_if_no_tile} 48 #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set": 49 #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default": 50 --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}" 51 #end if 52 #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default": 53 --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}" 54 #end if 55 #end if 56 ${analysis_param_type.simplify_bam} 57 --preserve_qscores_less_than "${analysis_param_type.preserve_qscores_less_than}" 58 --smoothing "${analysis_param_type.smoothing}" 59 --max_quality_score "${analysis_param_type.max_quality_score}" 60 --window_size_nqs "${analysis_param_type.window_size_nqs}" 61 --homopolymer_nback "${analysis_param_type.homopolymer_nback}" 62 ${analysis_param_type.do_not_write_original_quals} 63 ' 64 #end if 65 </command> 66 <inputs> 67 <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> 68 <conditional name="reference_source"> 69 <expand macro="reference_source_selector_param" /> 70 <when value="cached"> 71 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;"> 72 <validator type="unspecified_build" /> 73 <validator type="dataset_metadata_in_data_table" table_name="gatk_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 --> 74 </param> 75 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" > 76 <options from_data_table="gatk_picard_indexes"> 77 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> 78 </options> 79 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 80 </param> 81 </when> 82 <when value="history"> 83 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" /> 84 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;"> 85 <options> 86 <filter type="data_meta" key="dbkey" ref="input_bam" /> 87 </options> 88 </param> 89 </when> 90 </conditional> 91 92 <expand macro="gatk_param_type_conditional" /> 93 94 95 <expand macro="analysis_type_conditional"> 96 <conditional name="default_read_group_type"> 97 <param name="default_read_group_type_selector" type="select" label="Set default Read Group" help="--default_read_group"> 98 <option value="default" selected="True">Don't Set</option> 99 <option value="set">Set</option> 100 </param> 101 <when value="default"> 102 <!-- do nothing here --> 103 </when> 104 <when value="set"> 105 <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/> 106 </when> 107 </conditional> 108 <param name="default_platform" type="select" label="Set default Platform" help="--default_platform"> 109 <option value="default" selected="True">Don't Set</option> 110 <option value="illumina">illumina</option> 111 <option value="454">454</option> 112 <option value="solid">solid</option> 113 </param> 114 <conditional name="force_read_group_type"> 115 <param name="force_read_group_type_selector" type="select" label="Force Read Group" help="--force_read_group"> 116 <option value="default" selected="True">Don't Force</option> 117 <option value="set">Force</option> 118 </param> 119 <when value="default"> 120 <!-- do nothing here --> 121 </when> 122 <when value="set"> 123 <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."/> 124 </when> 125 </conditional> 126 <param name="force_platform" type="select" label="Force Platform" help="--force_platform"> 127 <option value="default" selected="True">Don't Force</option> 128 <option value="illumina">illumina</option> 129 <option value="454">454</option> 130 <option value="solid">solid</option> 131 </param> 132 <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"/> 133 <conditional name="solid_options_type"> 134 <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options"> 135 <option value="default" selected="True">Don't Set</option> 136 <option value="set">Set</option> 137 </param> 138 <when value="default"> 139 <!-- do nothing here --> 140 </when> 141 <when value="set"> 142 <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;"> 143 <option value="default" selected="True">Don't set</option> 144 <option value="DO_NOTHING">DO_NOTHING</option> 145 <option value="SET_Q_ZERO">SET_Q_ZERO</option> 146 <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option> 147 <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option> 148 </param> 149 <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;"> 150 <option value="default" selected="True">Don't set</option> 151 <option value="THROW_EXCEPTION">THROW_EXCEPTION</option> 152 <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option> 153 <option value="PURGE_READ">PURGE_READ</option> 154 </param> 155 </when> 156 </conditional> 157 <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/> 158 <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="--window_size_nqs"/> 159 <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;" /> 160 <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;"/> 161 <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &lt;smoothing&gt;"/> 162 <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &lt;max_quality_score&gt;"/> 163 <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/> 164 </expand> 165 </inputs> 166 <outputs> 167 <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" /> 168 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 169 </outputs> 170 <tests> 171 <test> 172 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> 173 <param name="reference_source_selector" value="history" /> 174 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> 175 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" /> 176 <param name="gatk_param_type_selector" value="basic" /> 177 <param name="analysis_param_type_selector" value="basic" /> 178 <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" lines_diff="4" /> 179 <output name="output_log" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains" compare="contains" /> 180 </test> 181 </tests> 182 <help> 183**What it does** 184 185This 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. 186 187For more information on base quality score recalibration using the GATK, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration>`_. 188 189To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3>`_. 190 191If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_. 192 193------ 194 195**Inputs** 196 197GenomeAnalysisTK: TableRecalibration accepts an aligned BAM and a recalibration CSV input files. 198 199 200**Outputs** 201 202The output is in BAM format. 203 204 205Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. 206 207------- 208 209**Settings**:: 210 211 default_read_group If a read has no read group then default to the provided String. 212 default_platform If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid. 213 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. 214 force_platform If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid. 215 window_size_nqs The window size used by MinimumNQSCovariate for its calculation 216 homopolymer_nback The number of previous bases to look at in HomopolymerCovariate 217 exception_if_no_tile If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1 218 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) 219 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) 220 recal_file Filename for the input covariates table recalibration .csv file 221 out The output BAM file 222 bam_compression Compression level to use for writing BAM files 223 disable_bam_indexing Turn off on-the-fly creation of indices for output BAM files. 224 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 225 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 226 smoothing Number of imaginary counts to add to each bin bin order to smooth out bins with few data points, default=1 227 max_quality_score The integer value at which to cap the quality scores, default=50 228 doNotWriteOriginalQuals If true, we will not write the original quality (OQ) tag for each read 229 230@CITATION_SECTION@ 231 </help> 232</tool>