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

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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
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5:84584664264c 6:35c00763cb5c
1 <tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.0"> 1 <tool id="gatk2_variant_recalibrator" name="Variant Recalibrator" version="@VERSION@.1">
2 <description></description> 2 <description></description>
3 <macros>
4 <import>gatk2_macros.xml</import>
5 </macros>
3 <expand macro="requirements"> 6 <expand macro="requirements">
4 <requirement type="package" version="0.9.3">ggplot2</requirement> 7 <requirement type="package" version="0.9.3">ggplot2</requirement>
5 </expand> 8 </expand>
6 <macros> 9 <expand macro="version_command" />
7 <import>gatk2_macros.xml</import>
8 </macros>
9 <command interpreter="python"> 10 <command interpreter="python">
10 gatk2_wrapper.py 11 gatk2_wrapper.py
11 --stdout "${output_log}" 12 --stdout "${output_log}"
12 #for $var_count, $variant in enumerate( $reference_source.variants ): 13 #for $var_count, $variant in enumerate( $reference_source.input_variants ):
13 -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}" 14 -d "--input:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
14 #end for 15 #end for
15 -p ' 16 -p '
16 @JAR_PATH@ 17 @JAR_PATH@
17 -T "VariantRecalibrator" 18 -T "VariantRecalibrator"
18 \$GATK2_SITE_OPTIONS 19 \$GATK2_SITE_OPTIONS
24 #end if 25 #end if
25 --recal_file "${output_recal}" 26 --recal_file "${output_recal}"
26 --tranches_file "${output_tranches}" 27 --tranches_file "${output_tranches}"
27 --rscript_file "${output_rscript}" 28 --rscript_file "${output_rscript}"
28 ' 29 '
29 30
30 #set $rod_binding_names = dict() 31 #set $rod_binding_names = dict()
31 #for $rod_binding in $rod_bind: 32 #for $rod_binding in $rod_bind:
32 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom': 33 #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
33 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name 34 #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
34 #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp': 35 #elif str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'comp':
35 #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name 36 #set $rod_bind_name = "comp" + $rod_binding.rod_bind_type.custom_rod_name
36 #else 37 #else
37 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector 38 #set $rod_bind_name = $rod_binding.rod_bind_type.rod_bind_type_selector
38 #end if 39 #end if
39 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1 40 #set $rod_binding_names[$rod_bind_name] = $rod_binding_names.get( $rod_bind_name, -1 ) + 1
40 #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known": 41 #if $rod_binding.rod_bind_type.rod_training_type.rod_training_type_selector == "not_training_truth_known":
41 -d "--resource:${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[$rod_bind_name]}" 42 -d "--resource:${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[$rod_bind_name]}"
42 #else: 43 #else:
43 -d "--resource:${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]}" 44 -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[$rod_bind_name]}"
44 #end if 45 #end if
45 #end for 46 #end for
46 47
47 #include source=$standard_gatk_options# 48 #include source=$standard_gatk_options#
48 49
49 ##start analysis specific options 50 ##start analysis specific options
50 -p ' 51 -p '
51 #if str( $annotations ) != "None": 52 #if str( $annotations ) != "None":
52 #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ): 53 #for $annotation in str( $annotations.fields.gatk_value ).split( ',' ):
53 --use_annotation "${annotation}" 54 --use_annotation "${annotation}"
56 #for $additional_annotation in $additional_annotations: 57 #for $additional_annotation in $additional_annotations:
57 --use_annotation "${additional_annotation.additional_annotation_name}" 58 --use_annotation "${additional_annotation.additional_annotation_name}"
58 #end for 59 #end for
59 --mode "${mode}" 60 --mode "${mode}"
60 ' 61 '
61 62
62 #if $analysis_param_type.analysis_param_type_selector == "advanced": 63 #if $analysis_param_type.analysis_param_type_selector == "advanced":
63 -p ' 64 -p '
64 --maxGaussians "${analysis_param_type.max_gaussians}" 65 --maxGaussians "${analysis_param_type.max_gaussians}"
65 --maxIterations "${analysis_param_type.max_iterations}" 66 --maxIterations "${analysis_param_type.max_iterations}"
66 --numKMeans "${analysis_param_type.num_k_means}" 67 --numKMeans "${analysis_param_type.num_k_means}"
82 #end if 83 #end if
83 --ignore_filter "${ignore_filter_name}" 84 --ignore_filter "${ignore_filter_name}"
84 #end for 85 #end for
85 ' 86 '
86 #end if 87 #end if
87 88
88
89 &amp;&amp; 89 &amp;&amp;
90 mv "${output_rscript}.pdf" "${output_tranches_pdf}" 90 mv "${output_rscript}.pdf" "${output_tranches_pdf}"
91 91
92 </command> 92 </command>
93 <inputs> 93 <inputs>
94 <conditional name="reference_source"> 94 <conditional name="reference_source">
95 <expand macro="reference_source_selector_param" /> 95 <expand macro="reference_source_selector_param" />
96 <when value="cached"> 96 <when value="cached">
97 <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;"> 97 <expand macro="input_variants" />
98 <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
99 </repeat>
100 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;"> 98 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
101 <options from_data_table="gatk2_picard_indexes"> 99 <options from_data_table="gatk2_picard_indexes">
102 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> --> 100 <!-- <filter type="data_meta" key="dbkey" ref="variants[0].input_variants" column="dbkey"/> -->
103 </options> 101 </options>
104 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 102 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
105 </param> 103 </param>
106 </when> 104 </when>
107 <when value="history"> <!-- FIX ME!!!! --> 105 <when value="history"> <!-- FIX ME!!!! -->
108 <repeat name="variants" title="Variant" min="1" help="-input,--input &amp;lt;input&amp;gt;"> 106 <expand macro="input_variants" />
109 <param name="input_variants" type="data" format="vcf" label="Variant file to recalibrate" />
110 </repeat>
111 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 107 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
112 </when> 108 </when>
113 </conditional> 109 </conditional>
114 110
115 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &amp;lt;resource&amp;gt;" min="2"> 111 <repeat name="rod_bind" title="Binding for reference-ordered data" help="-resource,--resource &amp;lt;resource&amp;gt;" min="2">
116 <conditional name="rod_bind_type"> 112 <conditional name="rod_bind_type">
117 <param name="rod_bind_type_selector" type="select" label="Binding Type"> 113 <param name="rod_bind_type_selector" type="select" label="Binding Type">
118 <option value="dbsnp" selected="True">dbSNP</option> 114 <option value="dbsnp" selected="True">dbSNP</option>
119 <option value="variant">Variants</option> 115 <option value="variant">Variants</option>
180 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/> 176 <param name="truth" type="boolean" label="Is Truth Site" truevalue="true" falsevalue="false"/>
181 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/> 177 <param name="bad" type="boolean" label="Is Bad Site" truevalue="true" falsevalue="false"/>
182 <param name="prior" type="float" label="prior probability of being true" value="12.0"/> 178 <param name="prior" type="float" label="prior probability of being true" value="12.0"/>
183 </when> 179 </when>
184 </conditional> 180 </conditional>
185 </when> 181 </when>
186 <when value="dbsnp"> 182 <when value="dbsnp">
187 <param name="input_rod" type="data" format="vcf" label="ROD file" /> 183 <param name="input_rod" type="data" format="vcf" label="ROD file" />
188 <conditional name="rod_training_type"> 184 <conditional name="rod_training_type">
189 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites"> 185 <param name="rod_training_type_selector" type="select" label="Use as training/truth/known sites">
190 <option value="is_training_truth_known">Set training/truth/known sites</option> 186 <option value="is_training_truth_known">Set training/truth/known sites</option>
298 </when> 294 </when>
299 </conditional> 295 </conditional>
300 </when> 296 </when>
301 </conditional> 297 </conditional>
302 </repeat> 298 </repeat>
303 299
304 <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;"> 300 <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;">
305 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> 301 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
306 <options from_data_table="gatk2_annotations"> 302 <options from_data_table="gatk2_annotations">
307 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> 303 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
308 <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/> 304 <filter type="static_value" value="VariantRecalibrator" column="tools_valid_for"/>
309 </options> 305 </options>
310 </param> 306 </param>
311 307
312 <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;"> 308 <repeat name="additional_annotations" title="Additional annotation" help="-an,--use_annotation &amp;lt;use_annotation&amp;gt;">
313 <param name="additional_annotation_name" type="text" value="" label="Annotation name" /> 309 <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
314 </repeat> 310 </repeat>
315 311
316 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;"> 312 <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
317 <option value="SNP" selected="True">SNP</option> 313 <option value="SNP" selected="True">SNP</option>
318 <option value="INDEL">INDEL</option> 314 <option value="INDEL">INDEL</option>
319 <option value="BOTH">BOTH</option> 315 <option value="BOTH">BOTH</option>
320 </param> 316 </param>
321 317
322 <expand macro="gatk_param_type_conditional" /> 318 <expand macro="gatk_param_type_conditional" />
323 319
324 <expand macro="analysis_type_conditional"> 320 <expand macro="analysis_type_conditional">
325 <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;"/> 321 <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;"/>
326 <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;"/> 322 <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;"/>
327 <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;"/> 323 <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;"/>
328 <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;"/> 324 <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;"/>