/tools/gatk/variant_apply_recalibration.xml
https://bitbucket.org/cistrome/cistrome-harvard/ · XML · 139 lines · 115 code · 22 blank · 2 comment · 0 complexity · 2e1de3a1d164f465a9a9db2367c795b4 MD5 · raw file
- <tool id="gatk_variant_apply_recalibration" name="Apply Variant Recalibration" version="0.0.4">
- <description></description>
- <requirements>
- <requirement type="package" version="1.4">gatk</requirement>
- </requirements>
- <macros>
- <import>gatk_macros.xml</import>
- </macros>
- <command interpreter="python">gatk_wrapper.py
- --max_jvm_heap_fraction "1"
- --stdout "${output_log}"
- #for $var_count, $variant in enumerate( $reference_source.variants ):
- -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
- #end for
- -p 'java
- -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
- -T "ApplyRecalibration"
- ##--num_threads 4 ##hard coded, for now
- -et "NO_ET" ##ET no phone home
- #if $reference_source.reference_source_selector != "history":
- -R "${reference_source.ref_file.fields.path}"
- #end if
- --recal_file "${reference_source.input_recal}"
- --tranches_file "${reference_source.input_tranches}"
- --out "${output_variants}"
- '
-
- #include source=$standard_gatk_options#
-
- ##start analysis specific options
- -p '
- --mode "${mode}"
-
- #for $ignore_filter in $ignore_filters:
- #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
- #if $ignore_filter_name == "custom":
- #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
- #end if
- --ignore_filter "${ignore_filter_name}"
- #end for
- --ts_filter_level "${ts_filter_level}"
- '
- </command>
- <inputs>
- <conditional name="reference_source">
- <expand macro="reference_source_selector_param" />
- <when value="cached">
- <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;">
- <param name="input_variants" type="data" format="vcf" label="Variant file to annotate"/>
- </repeat>
- <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" />
- <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" />
- <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &lt;reference_sequence&gt;">
- <options from_data_table="gatk_picard_indexes">
- <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
- </options>
- <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
- </param>
- </when>
- <when value="history"> <!-- FIX ME!!!! -->
- <repeat name="variants" title="Variant" min="1" help="-input,--input &lt;input&gt;">
- <param name="input_variants" type="data" format="vcf" label="Variant file to annotate" />
- </repeat>
- <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &lt;recal_file&gt;" />
- <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &lt;tranches_file&gt;" />
- <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &lt;reference_sequence&gt;" />
- </when>
- </conditional>
-
- <expand macro="gatk_param_type_conditional" />
-
- <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &lt;mode&gt;">
- <option value="SNP" selected="True">SNP</option>
- <option value="INDEL">INDEL</option>
- <option value="BOTH">BOTH</option>
- </param>
- <repeat name="ignore_filters" title="Ignore Filter" help="-ignoreFilter,--ignore_filter &lt;ignore_filter&gt;">
- <conditional name="ignore_filter_type">
- <param name="ignore_filter_type_selector" type="select" label="Filter Type">
- <option value="HARD_TO_VALIDATE">HARD_TO_VALIDATE</option>
- <option value="LowQual" >LowQual</option>
- <option value="custom" selected="True">Other</option>
- </param>
- <when value="custom">
- <param name="filter_name" type="text" value="" label="Filter name"/>
- </when>
- <when value="HARD_TO_VALIDATE" />
- <when value="LowQual" />
- </conditional>
- </repeat>
- <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;"/>
- </inputs>
- <outputs>
- <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (Variants File)" />
- <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
- </outputs>
- <tests>
- <!-- ADD TESTS -->
- </tests>
- <help>
- **What it does**
- Applies cuts to the input vcf file (by adding filter lines) to achieve the desired novel FDR levels which were specified during VariantRecalibration
- For more information on using the ApplyRecalibration module, see this `tool specific page <http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration>`_.
- To 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>`_.
- If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gsa/wiki/index.php/Frequently_Asked_Questions>`_.
- ------
- **Inputs**
- GenomeAnalysisTK: ApplyRecalibration accepts a variant input file, a recalibration file and a tranches file.
- **Outputs**
- The output is in VCF format.
- Go `here <http://www.broadinstitute.org/gsa/wiki/index.php/Input_files_for_the_GATK>`_ for details on GATK file formats.
- -------
- **Settings**::
- recal_file The output recal file used by ApplyRecalibration
- tranches_file The input tranches file describing where to cut the data
- out The output filtered, recalibrated VCF file
- ts_filter_level The truth sensitivity level at which to start filtering
- ignore_filter If specified the optimizer will use variants even if the specified filter name is marked in the input VCF file
- 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)
- @CITATION_SECTION@
- </help>
- </tool>