Mercurial > repos > scisjnu123 > ngsap_vc
view GATK/gatk/realigner_target_creator.xml @ 2:2c7824a8d764 draft
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author | scisjnu123 |
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date | Thu, 12 Sep 2019 06:50:21 -0400 |
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<macros> <xml name="RealignerTargetCreatorParameters" tokens="tag"> <expand macro="macro_bam_input" tag="@TAG@" /> <expand macro="macro_optional_parameters"> <param name="maxIntervalSize" type="integer" value="500" label="maximum interval size; any intervals larger than this value will be dropped" help="-maxInterval,‑‑maxIntervalSize &lt;maxIntervalSize&gt;" /> <param name="minReadsAtLocus" type="integer" value="4" label="minimum reads at a locus to enable using the entropy calculation" help="-minReads,‑‑minReadsAtLocus &lt;minReadsAtLocus&gt;" /> <param name="windowSize" type="integer" value="10" label="window size for calculating entropy or SNP clusters" help="-window,‑‑windowSize &lt;windowSize&gt;" /> <param name="mismatchFraction" type="float" value="0.0" label="fraction of base qualities needing to mismatch for a position to have high entropy" help="-mismatch,‑‑mismatchFraction &lt;mismatchFraction&gt;" /> <repeat name="rod_bindings" title="Input VCF files with known indels" help="-known,‑‑known &lt;known&gt;"> <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" /> </repeat> </expand> </xml> <xml name="RealignerTargetCreatorOutput"> <data format="gatk_interval" name="rtc_output_intervals" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (GATK intervals)"> <yield /> </data> </xml> <template name="RealignerTargetCreatorPreprocessing"> <![CDATA[ @token_bam_input_pre@ #if $analysis_type.optional_parameters.optional_parameters_enabled #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings): ln -s -f ${rod_binding.input_rod} rod_binding_${i}.vcf && #end for #end if ]]> </template> <template name="RealignerTargetCreatorOptions"> <![CDATA[ --out ${rtc_output_intervals} @token_bam_input@ #if $analysis_type.optional_parameters.optional_parameters_enabled --maxIntervalSize ${analysis_type.optional_parameters.maxIntervalSize} --minReadsAtLocus ${analysis_type.optional_parameters.minReadsAtLocus} --windowSize ${analysis_type.optional_parameters.windowSize} --mismatchFraction ${analysis_type.optional_parameters.mismatchFraction} #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings): --known rod_binding_${i}.vcf #end for #end if ]]> </template> </macros>