/tools/gatk/variant_apply_recalibration.xml
XML | 139 lines | 115 code | 22 blank | 2 comment | 0 complexity | 2e1de3a1d164f465a9a9db2367c795b4 MD5 | raw file
1<tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.4"> 2 <description></description> 3 <requirements> 4 <requirement type="package" version="1.4">gatk</requirement> 5 </requirements> 6 <macros> 7 <import>gatk_macros.xml</import> 8 </macros> 9 <command interpreter="python">gatk_wrapper.py 10 --max_jvm_heap_fraction "1" 11 --stdout "${output_log}" 12 #for $var_count, $variant in enumerate( $reference_source.variants ): 13 -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" 14 #end for 15 -p 'java 16 -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" 17 -T "ApplyRecalibration" 18 ##--num_threads 4 ##hard coded, for now 19 -et "NO_ET" ##ET no phone home 20 #if $reference_source.reference_source_selector != "history": 21 -R "${reference_source.ref_file.fields.path}" 22 #end if 23 --recal_file "${reference_source.input_recal}" 24 --tranches_file "${reference_source.input_tranches}" 25 --out "${output_variants}" 26 ' 27 28 #include source=$standard_gatk_options# 29 30 ##start analysis specific options 31 -p ' 32 --mode "${mode}" 33 34 #for $ignore_filter in $ignore_filters: 35 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector ) 36 #if $ignore_filter_name == "custom": 37 #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name ) 38 #end if 39 --ignore_filter "${ignore_filter_name}" 40 #end for 41 --ts_filter_level "${ts_filter_level}" 42 ' 43 </command> 44 <inputs> 45 <conditional name="reference_source"> 46 <expand macro="reference_source_selector_param" /> 47 <when value="cached"> 48 <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> 49 <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/> 50 </repeat> 51 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> 52 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" /> 53 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;"> 54 <options from_data_table="gatk_picard_indexes"> 55 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> 56 </options> 57 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 58 </param> 59 </when> 60 <when value="history"> <!-- FIX ME!!!! --> 61 <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;"> 62 <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" /> 63 </repeat> 64 <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" /> 65 <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" /> 66 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" /> 67 </when> 68 </conditional> 69 70 <expand macro="gatk_param_type_conditional" /> 71 72 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;"> 73 <option value="SNP" selected="True">SNP</option> 74 <option value="INDEL">INDEL</option> 75 <option value="BOTH">BOTH</option> 76 </param> 77 <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;"> 78 <conditional name="ignore_filter_type"> 79 <param name="ignore_filter_type_selector" type="select" label="Filter Type"> 80 <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option> 81 <option value="LowQual" >LowQual</option> 82 <option value="custom" selected="True">Other</option> 83 </param> 84 <when value="custom"> 85 <param name="filter_name" type="text" value="" label="Filter name"/> 86 </when> 87 <when value="HARD_TO_VALIDATE" /> 88 <when value="LowQual" /> 89 </conditional> 90 </repeat> 91 <param name="ts_filter_level" type="float" label="truth sensitivity level at which to start filtering, used here to indicate filtered variants in plots" value="99.0" help="-ts_filter_level,--ts_filter_level &lt;ts_filter_level&gt;"/> 92 </inputs> 93 <outputs> 94 <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (Variants File)" /> 95 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 96 </outputs> 97 <tests> 98 <!-- ADD TESTS --> 99 </tests> 100 <help> 101**What it does** 102 103Applies cuts to the input vcf file (by adding filter lines) to achieve the desired novel FDR levels which were specified during VariantRecalibration 104 105For more information on using the ApplyRecalibration module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration>`_. 106 107To 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>`_. 108 109If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_. 110 111------ 112 113**Inputs** 114 115GenomeAnalysisTK: ApplyRecalibration accepts a variant input file, a recalibration file and a tranches file. 116 117 118**Outputs** 119 120The output is in VCF format. 121 122 123Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats. 124 125------- 126 127**Settings**:: 128 129 130 recal_file The output recal file used by ApplyRecalibration 131 tranches_file The input tranches file describing where to cut the data 132 out The output filtered, recalibrated VCF file 133 ts_filter_level The truth sensitivity level at which to start filtering 134 ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file 135 mode Recalibration mode to employ: 1.) SNP for recalibrating only SNPs (emitting indels untouched in the output VCF); 2.) INDEL for indels; and 3.) BOTH for recalibrating both SNPs and indels simultaneously. (SNP|INDEL|BOTH) 136 137@CITATION_SECTION@ 138 </help> 139</tool>