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comparison variant_eval.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 f244b8209eb8
children
comparison
equal deleted inserted replaced
5:84584664264c 6:35c00763cb5c
1 <tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.0"> 1 <tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.1">
2 <description></description> 2 <description></description>
3 <expand macro="requirements" />
4 <macros> 3 <macros>
5 <import>gatk2_macros.xml</import> 4 <import>gatk2_macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
7 <command interpreter="python"> 8 <command interpreter="python">
8 #from binascii import hexlify 9 #from binascii import hexlify
9 10
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( $reference_source.input_variants ):
13 -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}" 14 -d "--eval:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
14 #end for 15 #end for
15 -p ' 16 -p '
16 @JAR_PATH@ 17 @JAR_PATH@
17 -T "VariantEval" 18 -T "VariantEval"
18 --out "${output_report}" 19 --out "${output_report}"
22 23
23 #if $reference_source.reference_source_selector != "history": 24 #if $reference_source.reference_source_selector != "history":
24 -R "${reference_source.ref_file.fields.path}" 25 -R "${reference_source.ref_file.fields.path}"
25 #end if 26 #end if
26 ' 27 '
27 28
28 #for $rod_binding in $comp_rod_bind: 29 #for $rod_binding in $comp_rod_bind:
29 -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}" 30 -d "--comp:${rod_binding.comp_rod_name},%(file_type)s" "${rod_binding.comp_input_rod}" "${rod_binding.comp_input_rod.ext}" "input_comp_${rod_binding.comp_rod_name}"
30 #if str( $rod_binding.comp_known_names ): 31 #if str( $rod_binding.comp_known_names ):
31 -p '--known_names "${rod_binding.comp_rod_name}"' 32 -p '--known_names "${rod_binding.comp_rod_name}"'
32 #end if 33 #end if
33 #end for 34 #end for
34 35
35 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp' 36 #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp'
36 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}" 37 -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
37 #if $dbsnp_rod_bind_type.dbsnp_known_names 38 #if $dbsnp_rod_bind_type.dbsnp_known_names
38 -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"' 39 -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
39 #end if 40 #end if
40 #end if 41 #end if
41 42
42 #include source=$standard_gatk_options# 43 #include source=$standard_gatk_options#
43 44
44
45 ##start analysis specific options 45 ##start analysis specific options
46 #if $analysis_param_type.analysis_param_type_selector == "advanced": 46 #if $analysis_param_type.analysis_param_type_selector == "advanced":
47 #for $stratification in $analysis_param_type.stratifications: 47 #for $stratification in $analysis_param_type.stratifications:
48 #set $select_string = "--select_exps '%s' --select_names '%s'" % ( str( $stratification.select_exps ), str( $stratification.select_name ) ) 48 #set $select_string = "--select_exps '%s' --select_names '%s'" % ( str( $stratification.select_exps ), str( $stratification.select_name ) )
49 -o '${ hexlify( $select_string ) }' 49 -o '${ hexlify( $select_string ) }'
50 #end for 50 #end for
51 -p ' 51 -p '
52 52
53 #for $sample in $analysis_param_type.samples: 53 #for $sample in $analysis_param_type.samples:
54 --sample "${sample.sample}" 54 --sample "${sample.sample}"
55 #end for 55 #end for
56 56
57 #if str( $analysis_param_type.stratification_modules ) != "None": 57 #if str( $analysis_param_type.stratification_modules ) != "None":
58 #for $stratification_module in str( $analysis_param_type.stratification_modules).split( ',' ): 58 #for $stratification_module in str( $analysis_param_type.stratification_modules).split( ',' ):
59 --stratificationModule "${stratification_module}" 59 --stratificationModule "${stratification_module}"
60 #end for 60 #end for
61 #end if 61 #end if
62 62
63 ${analysis_param_type.do_not_use_all_standard_stratifications} 63 ${analysis_param_type.do_not_use_all_standard_stratifications}
64 64
65 #for $variant_type in $analysis_param_type.only_variants_of_type: 65 #for $variant_type in $analysis_param_type.only_variants_of_type:
66 --onlyVariantsOfType "${variant_type.variant_type}" 66 --onlyVariantsOfType "${variant_type.variant_type}"
67 #end for 67 #end for
68 68
69 #if str( $analysis_param_type.eval_modules ) != "None": 69 #if str( $analysis_param_type.eval_modules ) != "None":
70 #for $eval_module in str( $analysis_param_type.eval_modules).split( ',' ): 70 #for $eval_module in str( $analysis_param_type.eval_modules).split( ',' ):
71 --evalModule "${eval_module}" 71 --evalModule "${eval_module}"
72 #end for 72 #end for
73 #end if 73 #end if
74 74
75 ${analysis_param_type.do_not_use_all_standard_modules} 75 ${analysis_param_type.do_not_use_all_standard_modules}
76 76
77 #if str( $analysis_param_type.num_samples ) != "0": 77 #if str( $analysis_param_type.num_samples ) != "0":
78 --numSamples "${analysis_param_type.num_samples}" 78 --numSamples "${analysis_param_type.num_samples}"
79 #end if 79 #end if
80 80
81 --minPhaseQuality "${analysis_param_type.min_phase_quality}" 81 --minPhaseQuality "${analysis_param_type.min_phase_quality}"
82 82
83 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}" 83 --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}"
84 84
85 #if str( $analysis_param_type.ancestral_alignments ) != "None": 85 #if str( $analysis_param_type.ancestral_alignments ) != "None":
86 --ancestralAlignments "${analysis_param_type.ancestral_alignments}" 86 --ancestralAlignments "${analysis_param_type.ancestral_alignments}"
87 #end if 87 #end if
88 ' 88 '
89 #if str( $analysis_param_type.known_cnvs ) != "None": 89 #if str( $analysis_param_type.known_cnvs ) != "None":
90 -d "--knownCNVs" "${analysis_param_type.known_cnvs}" "${analysis_param_type.known_cnvs.ext}" "input_known_cnvs" 90 -d "--knownCNVs" "${analysis_param_type.known_cnvs}" "${analysis_param_type.known_cnvs.ext}" "input_known_cnvs"
91 #end if 91 #end if
92 92
93 #if str( $analysis_param_type.strat_intervals ) != "None": 93 #if str( $analysis_param_type.strat_intervals ) != "None":
94 -d "--stratIntervals" "${analysis_param_type.strat_intervals}" "${analysis_param_type.strat_intervals.ext}" "input_strat_intervals" 94 -d "--stratIntervals" "${analysis_param_type.strat_intervals}" "${analysis_param_type.strat_intervals.ext}" "input_strat_intervals"
95 #end if 95 #end if
96 #end if 96 #end if
97 </command> 97 </command>
98 <inputs> 98 <inputs>
99 99
100 <conditional name="reference_source"> 100 <conditional name="reference_source">
101 <expand macro="reference_source_selector_param" /> 101 <expand macro="reference_source_selector_param" />
102 <when value="cached"> 102 <when value="cached">
103 <repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;"> 103 <expand macro="input_variants" help="-eval,--eval &amp;lt;eval&amp;gt;"/>
104 <param name="input_variant" type="data" format="vcf" label="Input variant file" />
105 </repeat>
106 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;"> 104 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
107 <options from_data_table="gatk2_picard_indexes"> 105 <options from_data_table="gatk2_picard_indexes">
108 <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> --> 106 <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
109 </options> 107 </options>
110 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 108 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
111 </param> 109 </param>
112 </when> 110 </when>
113 <when value="history"> <!-- FIX ME!!!! --> 111 <when value="history"> <!-- FIX ME!!!! -->
114 <repeat name="variants" title="Variant" min="1" help="-eval,--eval &amp;lt;eval&amp;gt;"> 112 <expand macro="input_variants" help="-eval,--eval &amp;lt;eval&amp;gt;" />
115 <param name="input_variant" type="data" format="vcf" label="Input variant file" />
116 </repeat>
117 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 113 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
118 </when> 114 </when>
119 </conditional> 115 </conditional>
120 116
121 <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &amp;lt;comp&amp;gt;"> 117 <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &amp;lt;comp&amp;gt;">
122 <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" /> 118 <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" />
123 <param name="comp_rod_name" type="text" value="" label="Comparison ROD name"> 119 <param name="comp_rod_name" type="text" value="" label="Comparison ROD name">
124 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> 120 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
125 </param> 121 </param>
137 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> 133 <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
138 </param> 134 </param>
139 <param name="dbsnp_known_names" type="boolean" label="Use dbSNP ROD file as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;" /> 135 <param name="dbsnp_known_names" type="boolean" label="Use dbSNP ROD file as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;" />
140 </when> 136 </when>
141 </conditional> 137 </conditional>
142 138
143 <expand macro="gatk_param_type_conditional" /> 139 <expand macro="gatk_param_type_conditional" />
144 140
145
146 <expand macro="analysis_type_conditional"> 141 <expand macro="analysis_type_conditional">
147 <repeat name="stratifications" title="Stratification"> 142 <repeat name="stratifications" title="Stratification">
148 <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &amp;lt;select_exps&amp;gt;"> 143 <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &amp;lt;select_exps&amp;gt;">
149 <sanitizer> 144 <sanitizer>
150 <valid initial="string.printable"> 145 <valid initial="string.printable">
153 <mapping initial="none"/> 148 <mapping initial="none"/>
154 </sanitizer> 149 </sanitizer>
155 </param> 150 </param>
156 <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names &amp;lt;select_names&amp;gt;"/> 151 <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names &amp;lt;select_names&amp;gt;"/>
157 </repeat> 152 </repeat>
158 153
159 <repeat name="samples" title="Sample" help="-sn,--sample &amp;lt;sample&amp;gt;"> 154 <repeat name="samples" title="Sample" help="-sn,--sample &amp;lt;sample&amp;gt;">
160 <param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/> 155 <param name="sample" value="" type="text" label="Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context"/>
161 </repeat> 156 </repeat>
162 157
163 <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &amp;lt;stratificationModule&amp;gt;" > 158 <param name="stratification_modules" type="select" multiple="True" display="checkboxes" label="Stratification modules to apply to the eval track(s)" help="-ST,--stratificationModule &amp;lt;stratificationModule&amp;gt;" >
164 <option value="AlleleCount" /> 159 <option value="AlleleCount" />
165 <option value="AlleleFrequency" /> 160 <option value="AlleleFrequency" />
166 <option value="CompRod" /> 161 <option value="CompRod" />
167 <option value="Contig" /> 162 <option value="Contig" />
179 <option value="SnpEffPositionModifier" /> 174 <option value="SnpEffPositionModifier" />
180 <option value="TandemRepeat" /> 175 <option value="TandemRepeat" />
181 <option value="VariantType" /> 176 <option value="VariantType" />
182 </param> 177 </param>
183 <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" help="-noST,--doNotUseAllStandardStratifications" /> 178 <param name="do_not_use_all_standard_stratifications" checked="false" type="boolean" truevalue="--doNotUseAllStandardStratifications" falsevalue="" label="Do not use the standard stratification modules by default" help="-noST,--doNotUseAllStandardStratifications" />
184 179
185 <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType"> 180 <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType">
186 <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/> 181 <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/>
187 </repeat> 182 </repeat>
188 183
189 <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &amp;lt;evalModule&amp;gt;" > 184 <param name="eval_modules" type="select" multiple="True" display="checkboxes" label="Eval modules to apply to the eval track(s)" help="-EV,--evalModule &amp;lt;evalModule&amp;gt;" >
190 <option value="CompOverlap" /> 185 <option value="CompOverlap" />
191 <option value="CountVariants" /> 186 <option value="CountVariants" />
192 <option value="IndelLengthHistogram" /> 187 <option value="IndelLengthHistogram" />
193 <option value="IndelSummary" /> 188 <option value="IndelSummary" />
198 <option value="TiTvVariantEvaluator" /> 193 <option value="TiTvVariantEvaluator" />
199 <option value="ValidationReport" /> 194 <option value="ValidationReport" />
200 <option value="VariantSummary" /> 195 <option value="VariantSummary" />
201 </param> 196 </param>
202 <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" help="-noEV,--doNotUseAllStandardModules" /> 197 <param name="do_not_use_all_standard_modules" checked="false" type="boolean" truevalue="--doNotUseAllStandardModules" falsevalue="" label="Do not use the standard eval modules by default" help="-noEV,--doNotUseAllStandardModules" />
203 198
204 <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file" value="0" help="-ns,--numSamples &amp;lt;numSamples&amp;gt;"/> 199 <param name="num_samples" type="integer" label="Number of samples (used if no samples are available in the VCF file" value="0" help="-ns,--numSamples &amp;lt;numSamples&amp;gt;"/>
205 <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &amp;lt;minPhaseQuality&amp;gt;"/> 200 <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &amp;lt;minPhaseQuality&amp;gt;"/>
206 <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50" help="-mvq,--mendelianViolationQualThreshold &amp;lt;mendelianViolationQualThreshold&amp;gt;"/> 201 <param name="mendelian_violation_qual_threshold" type="integer" label="Minimum genotype QUAL score for each trio member required to accept a site as a violation" value="50" help="-mvq,--mendelianViolationQualThreshold &amp;lt;mendelianViolationQualThreshold&amp;gt;"/>
207 <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &amp;lt;ancestralAlignments&amp;gt;" /> 202 <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &amp;lt;ancestralAlignments&amp;gt;" />
208 <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs &amp;lt;knownCNVs&amp;gt;" /> 203 <param name="known_cnvs" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features describing a known list of copy number variants" help="-knownCNVs,--knownCNVs &amp;lt;knownCNVs&amp;gt;" />
209 <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals &amp;lt;stratIntervals&amp;gt;" /> 204 <param name="strat_intervals" type="data" format="bed,gatk_interval,picard_interval_list" optional="True" label="File containing tribble-readable features for the IntervalStratificiation" help="-stratIntervals,--stratIntervals &amp;lt;stratIntervals&amp;gt;" />
210
211 </expand> 205 </expand>
212 206
213
214 </inputs> 207 </inputs>
215 <outputs> 208 <outputs>
216 <data format="gatk_report" name="output_report" label="${tool.name} on ${on_string} (report)" /> 209 <data format="gatk_report" name="output_report" label="${tool.name} on ${on_string} (report)" />
217 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 210 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
218 </outputs> 211 </outputs>
267 select_names Names to use for the list of stratifications (must be a 1-to-1 mapping) 260 select_names Names to use for the list of stratifications (must be a 1-to-1 mapping)
268 sample Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context 261 sample Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context
269 known_names Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets 262 known_names Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets
270 stratificationModule One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified) 263 stratificationModule One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)
271 doNotUseAllStandardStratifications Do not use the standard stratification modules by default (instead, only those that are specified with the -S option) 264 doNotUseAllStandardStratifications Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)
272 onlyVariantsOfType If provided, only variants of these types will be considered during the evaluation, in 265 onlyVariantsOfType If provided, only variants of these types will be considered during the evaluation, in
273 evalModule One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified) 266 evalModule One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)
274 doNotUseAllStandardModules Do not use the standard modules by default (instead, only those that are specified with the -E option) 267 doNotUseAllStandardModules Do not use the standard modules by default (instead, only those that are specified with the -E option)
275 numSamples Number of samples (used if no samples are available in the VCF file 268 numSamples Number of samples (used if no samples are available in the VCF file
276 minPhaseQuality Minimum phasing quality 269 minPhaseQuality Minimum phasing quality
277 mendelianViolationQualThreshold Minimum genotype QUAL score for each trio member required to accept a site as a violation 270 mendelianViolationQualThreshold Minimum genotype QUAL score for each trio member required to accept a site as a violation