/tools/gatk/realigner_target_creator.xml
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1<tool id="gatk_realigner_target_creator" name="Realigner Target Creator" version="0.0.4"> 2 <description>for use in local realignment</description> 3 <requirements> 4 <requirement type="package" version="1.3">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 "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" 19 -T "RealignerTargetCreator" 20 -o "${output_interval}" 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 ' 28 #set $rod_binding_names = dict() 29 #for $rod_binding in $rod_bind: 30 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': 31 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name 32 #else 33 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector 34 #end if 35 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 36 -d "-known:${rod_bind_name},%(file_type)s" "${rod_binding.rod_bind_type.input_rod}" "${rod_binding.rod_bind_type.input_rod.ext}" "input_${rod_bind_name}_${rod_binding_names[$rod_bind_name]}" 37 #end for 38 39 #include source=$standard_gatk_options# 40 ##start analysis specific options 41 #if $analysis_param_type.analysis_param_type_selector == "advanced": 42 -p ' 43 --minReadsAtLocus "${analysis_param_type.minReadsAtLocus}" 44 --windowSize "${analysis_param_type.windowSize}" 45 --mismatchFraction "${analysis_param_type.mismatchFraction}" 46 --maxIntervalSize "${analysis_param_type.maxIntervalSize}" 47 ' 48 #end if 49 </command> 50 <inputs> 51 <conditional name="reference_source"> 52 <expand macro="reference_source_selector_param" /> 53 <when value="cached"> 54 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;"> 55 <validator type="unspecified_build" /> 56 <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 --> 57 </param> 58 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;" > 59 <options from_data_table="gatk_picard_indexes"> 60 <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> 61 </options> 62 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 63 </param> 64 </when> 65 <when value="history"> 66 <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &lt;input_file&gt;" /> 67 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;"> 68 <options> 69 <filter type="data_meta" key="dbkey" ref="input_bam" /> 70 </options> 71 </param> 72 </when> 73 </conditional> 74 75 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-known,--known &lt;known&gt;"> 76 <conditional name="rod_bind_type"> 77 <param name="rod_bind_type_selector" type="select" label="Binding Type"> 78 <option value="dbsnp" selected="True">dbSNP</option> 79 <option value="snps">SNPs</option> 80 <option value="indels">INDELs</option> 81 <option value="custom">Custom</option> 82 </param> 83 <when value="dbsnp"> 84 <param name="input_rod" type="data" format="vcf" label="ROD file" /> 85 </when> 86 <when value="snps"> 87 <param name="input_rod" type="data" format="vcf" label="ROD file" /> 88 </when> 89 <when value="indels"> 90 <param name="input_rod" type="data" format="vcf" label="ROD file" /> 91 </when> 92 <when value="custom"> 93 <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/> 94 <param name="input_rod" type="data" format="vcf" label="ROD file" /> 95 </when> 96 </conditional> 97 </repeat> 98 99 <expand macro="gatk_param_type_conditional" /> 100 101 <expand macro="analysis_type_conditional"> 102 <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize &lt;windowSize&gt;" /> 103 <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to <= 0 or > 1 (-mismatch,--mismatchFraction &lt;mismatchFraction&gt;)"/> 104 <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus &lt;minReadsAtLocus&gt;" /> 105 <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &lt;maxIntervalSize&gt;" /> 106 </expand> 107 </inputs> 108 <outputs> 109 <data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" /> 110 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 111 </outputs> 112 <tests> 113 <test> 114 <param name="reference_source_selector" value="history" /> 115 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> 116 <param name="input_bam" value="gatk/fake_phiX_reads_1.bam" ftype="bam" /> 117 <param name="rod_bind_type_selector" value="dbsnp" /> 118 <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /> 119 <param name="gatk_param_type_selector" value="basic" /> 120 <param name="analysis_param_type_selector" value="advanced" /> 121 <param name="windowSize" value="10" /> 122 <param name="mismatchFraction" value="0.15" /> 123 <param name="minReadsAtLocus" value="4" /> 124 <param name="maxIntervalSize" value="500" /> 125 <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" /> 126 <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/> 127 </test> 128 </tests> 129 <help> 130**What it does** 131 132Emits intervals for the Local Indel Realigner to target for cleaning. Ignores 454 reads, MQ0 reads, and reads with consecutive indel operators in the CIGAR string. 133 134For more information on local realignment around indels using the GATK, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels>`_. 135 136To 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>`_. 137 138If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_. 139 140------ 141 142**Inputs** 143 144GenomeAnalysisTK: RealignerTargetCreator accepts an aligned BAM input file. 145 146 147**Outputs** 148 149The output is in GATK Interval format. 150 151 152Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. 153 154------- 155 156**Settings**:: 157 158 windowSize window size for calculating entropy or SNP clusters 159 mismatchFraction fraction of base qualities needing to mismatch for a position to have high entropy; to disable set to <= 0 or > 1 160 minReadsAtLocus minimum reads at a locus to enable using the entropy calculation 161 maxIntervalSize maximum interval size 162 163@CITATION_SECTION@ 164 </help> 165</tool>