gatk2: variant_recalibrator.xml comparison

comparison variant_recalibrator.xml @ 6:35c00763cb5c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33

author	iuc
date	Mon, 04 Jun 2018 05:38:15 -0400
parents	84584664264c
children

comparison

equal deleted inserted replaced

-:84584664264c
+:35c00763cb5c
-<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.0">
+<tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.1">
 <description></description>
+<macros>
+<import>gatk2_macros.xml</import>
+</macros>
 <expand macro="requirements">
 <requirement type="package" version="0.9.3">ggplot2</requirement>
 </expand>
-<macros>
+<expand macro="version_command" />
-<import>gatk2_macros.xml</import>
-</macros>
 <command interpreter="python">
 gatk2_wrapper.py
 --stdout "${output_log}"
-#for $var_count, $variant in enumerate( $reference_source.variants ):
+#for $var_count, $variant in enumerate( $reference_source.input_variants ):
--d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
+-d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
 #end for
 -p '
 @JAR_PATH@
 -T "VariantRecalibrator"
 \$GATK2_SITE_OPTIONS
 #end if
 --recal_file "${output_recal}"
 --tranches_file "${output_tranches}"
 --rscript_file "${output_rscript}"
 '
 #set $rod_binding_names = dict()
 #for $rod_binding in $rod_bind:
 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
 #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
 #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name
 #else
 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
 #end if
 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
 #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known":
 -d "--resource:${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[$rod_bind_name]}"
 #else:
 -d "--resource:${rod_bind_name},%(file_type)s,known=${rod_binding.rod_bind_type.rod_training_type.known},training=${rod_binding.rod_bind_type.rod_training_type.training},truth=${rod_binding.rod_bind_type.rod_training_type.truth},bad=${rod_binding.rod_bind_type.rod_training_type.bad},prior=${rod_binding.rod_bind_type.rod_training_type.prior}" "${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]}"
 #end if
 #end for
 #include source=$standard_gatk_options#
 ##start analysis specific options
 -p '
 #if str( $annotations ) != "None":
 #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ):
 --use_annotation "${annotation}"
 #for $additional_annotation in $additional_annotations:
 --use_annotation "${additional_annotation.additional_annotation_name}"
 #end for
 --mode "${mode}"
 '
 #if $analysis_param_type.analysis_param_type_selector == "advanced":
 -p '
 --maxGaussians "${analysis_param_type.max_gaussians}"
 --maxIterations "${analysis_param_type.max_iterations}"
 --numKMeans "${analysis_param_type.num_k_means}"
 #end if
 --ignore_filter "${ignore_filter_name}"
 #end for
 '
 #end if
 &amp;&amp;
 mv "${output_rscript}.pdf" "${output_tranches_pdf}"
 </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 &amp;lt;input&amp;gt;">
+<expand macro="input_variants" />
-<param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
-</repeat>
 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
 <options from_data_table="gatk2_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 &amp;lt;input&amp;gt;">
+<expand macro="input_variants" />
-<param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
-</repeat>
 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
 </when>
 </conditional>
 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &amp;lt;resource&amp;gt;" min="2">
 <conditional name="rod_bind_type">
 <param name="rod_bind_type_selector" type="select" label="Binding Type">
 <option value="dbsnp" selected="True">dbSNP</option>
 <option value="variant">Variants</option>
 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
 </when>
 </conditional>
 </when>
 <when value="dbsnp">
 <param name="input_rod" type="data" format="vcf" label="ROD file" />
 <conditional name="rod_training_type">
 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
 <option value="is_training_truth_known">Set training/truth/known sites</option>
 </when>
 </conditional>
 </when>
 </conditional>
 </repeat>
 <param name="annotations" type="select" multiple="True" display="checkboxes" label="annotations which should used for calculations" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
 <options from_data_table="gatk2_annotations">
 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
 <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
 </options>
 </param>
 <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
 </repeat>
 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
 <option value="SNP" selected="True">SNP</option>
 <option value="INDEL">INDEL</option>
 <option value="BOTH">BOTH</option>
 </param>
 <expand macro="gatk_param_type_conditional" />
 <expand macro="analysis_type_conditional">
 <param name="max_gaussians" type="integer" label="maximum number of Gaussians to try during variational Bayes Algorithm" value="8" help="-mG,--maxGaussians &amp;lt;maxGaussians&amp;gt;"/>
 <param name="max_iterations" type="integer" label="maximum number of maximum number of VBEM iterations to be performed in variational Bayes Algorithm" value="150" help="-mI,--maxIterations &amp;lt;maxIterations&amp;gt;"/>
 <param name="num_k_means" type="integer" label="number of k-means iterations to perform in order to initialize the means of the Gaussians in the Gaussian mixture model" value="100" help="-nKM,--numKMeans &amp;lt;numKMeans&amp;gt;"/>
 <param name="std_threshold" type="float" label="If a variant has annotations more than -std standard deviations away from mean then don't use it for building the Gaussian mixture model." value="10.0" help="-std,--stdThreshold &amp;lt;stdThreshold&amp;gt;"/>

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comparison variant_recalibrator.xml @ 6:35c00763cb5c draft default tip