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comparison unified_genotyper.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_unified_genotyper" name="Unified Genotyper" version="@VERSION@.0"> 1 <tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="@VERSION@.2">
2 <description>SNP and indel caller</description> 2 <description>SNP and indel caller</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 gatk2_wrapper.py 9 gatk2_wrapper.py
9 --stdout "${output_log}" 10 --stdout "${output_log}"
10 #for $i, $input_bam in enumerate( $reference_source.input_bams ): 11 @BAM_INPUTS@
11 -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
12 #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
13 -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
14 #end if
15 #end for
16 -p ' 12 -p '
17 @JAR_PATH@ 13 @JAR_PATH@
18 -T "UnifiedGenotyper" 14 -T "UnifiedGenotyper"
19 @THREADS@ 15 @THREADS@
20 --out "${output_vcf}" 16 --out "${output_vcf}"
30 --genotype_likelihoods_model "${genotype_likelihoods_model}" 26 --genotype_likelihoods_model "${genotype_likelihoods_model}"
31 --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}" 27 --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}"
32 --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}" 28 --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}"
33 ' 29 '
34 @DBSNP_OPTIONS@ 30 @DBSNP_OPTIONS@
35 31 $allow_n_cigar_reads
36 #include source=$standard_gatk_options# 32 #include source=$standard_gatk_options#
37 ##start analysis specific options 33 ##start analysis specific options
38 #if $analysis_param_type.analysis_param_type_selector == "advanced": 34 #if $analysis_param_type.analysis_param_type_selector == "advanced":
39 -p ' 35 -p '
40 --heterozygosity "${analysis_param_type.heterozygosity}" 36 --heterozygosity "${analysis_param_type.heterozygosity}"
86 </command> 82 </command>
87 <inputs> 83 <inputs>
88 <conditional name="reference_source"> 84 <conditional name="reference_source">
89 <expand macro="reference_source_selector_param" /> 85 <expand macro="reference_source_selector_param" />
90 <when value="cached"> 86 <when value="cached">
91 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;"> 87 <expand macro="input_bams_cached" />
92 <param name="input_bam" type="data" format="bam" label="BAM file">
93 <validator type="unspecified_build" />
94 <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
95 </param>
96 </repeat>
97 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;"> 88 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
98 <options from_data_table="gatk2_picard_indexes"> 89 <options from_data_table="gatk2_picard_indexes">
99 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 90 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
100 </options> 91 </options>
101 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 92 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
102 </param> 93 </param>
103 </when> 94 </when>
104 <when value="history"> <!-- FIX ME!!!! --> 95 <when value="history"> <!-- FIX ME!!!! -->
105 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;"> 96 <expand macro="input_bams_history" />
106 <param name="input_bam" type="data" format="bam" label="BAM file" >
107 </param>
108 </repeat>
109 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 97 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
110 </when> 98 </when>
111 </conditional> 99 </conditional>
112 <expand macro="dbsnp_param" /> 100 <expand macro="dbsnp_param" />
113 101
114 <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ" help="-glm,--genotype_likelihoods_model &amp;lt;genotype_likelihoods_model&amp;gt;"> 102 <param name="genotype_likelihoods_model" type="select" label="Genotype likelihoods calculation model to employ" help="-glm,--genotype_likelihoods_model &amp;lt;genotype_likelihoods_model&amp;gt;">
115 <option value="BOTH" selected="True">BOTH</option> 103 <option value="BOTH" selected="True">BOTH</option>
116 <option value="SNP">SNP</option> 104 <option value="SNP">SNP</option>
117 <option value="INDEL">INDEL</option> 105 <option value="INDEL">INDEL</option>
118 </param> 106 </param>
119 107
120 <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" help="-stand_call_conf,--standard_min_confidence_threshold_for_calling &amp;lt;standard_min_confidence_threshold_for_calling&amp;gt;" /> 108 <param name="standard_min_confidence_threshold_for_calling" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called" help="-stand_call_conf,--standard_min_confidence_threshold_for_calling &amp;lt;standard_min_confidence_threshold_for_calling&amp;gt;" />
121 <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" help="-stand_emit_conf,--standard_min_confidence_threshold_for_emitting &amp;lt;standard_min_confidence_threshold_for_emitting&amp;gt;" /> 109 <param name="standard_min_confidence_threshold_for_emitting" type="float" value="30.0" label="The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)" help="-stand_emit_conf,--standard_min_confidence_threshold_for_emitting &amp;lt;standard_min_confidence_threshold_for_emitting&amp;gt;" />
122 110
123 111 <expand macro="allow_n_cigar_reads" />
124 <expand macro="gatk_param_type_conditional" /> 112 <expand macro="gatk_param_type_conditional" />
125 113
126 <expand macro="analysis_type_conditional"> 114 <expand macro="analysis_type_conditional">
127 <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus" help="-hets,--heterozygosity &amp;lt;heterozygosity&amp;gt;" /> 115 <param name="heterozygosity" type="float" value="1e-3" label="Heterozygosity value used to compute prior likelihoods for any locus"
128 <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods" help="-pcr_error,--pcr_error_rate &amp;lt;pcr_error_rate&amp;gt;" /> 116 help="-hets,--heterozygosity &amp;lt;heterozygosity&amp;gt;" />
117 <param name="pcr_error_rate" type="float" value="1e-4" label="The PCR error rate to be used for computing fragment-based likelihoods"
118 help="-pcr_error,--pcr_error_rate &amp;lt;pcr_error_rate&amp;gt;" />
129 <conditional name="genotyping_mode_type"> 119 <conditional name="genotyping_mode_type">
130 <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &amp;lt;genotyping_mode&amp;gt;"> 120 <param name="genotyping_mode" type="select" label="How to determine the alternate allele to use for genotyping" help="-gt_mode,--genotyping_mode &amp;lt;genotyping_mode&amp;gt;">
131 <option value="DISCOVERY" selected="True">DISCOVERY</option> 121 <option value="DISCOVERY" selected="True">DISCOVERY</option>
132 <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option> 122 <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
133 </param> 123 </param>
189 <option value="WorkInProgress">WorkInProgress</option> 179 <option value="WorkInProgress">WorkInProgress</option>
190 <option value="RankSumTest">RankSumTest</option> 180 <option value="RankSumTest">RankSumTest</option>
191 <!-- <option value="none">none</option> --> 181 <!-- <option value="none">none</option> -->
192 </param> 182 </param>
193 <!-- <param name="family_string" type="text" value="" label="Family String"/> --> 183 <!-- <param name="family_string" type="text" value="" label="Family String"/> -->
194 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" > 184 <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude"
185 help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&amp;gt;" >
195 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs --> 186 <!-- load the available annotations from an external configuration file, since additional ones can be added to local installs -->
196 <options from_data_table="gatk2_annotations"> 187 <options from_data_table="gatk2_annotations">
197 <filter type="multiple_splitter" column="tools_valid_for" separator=","/> 188 <filter type="multiple_splitter" column="tools_valid_for" separator=","/>
198 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/> 189 <filter type="static_value" value="UnifiedGenotyper" column="tools_valid_for"/>
199 </options> 190 </options>
200 </param> 191 </param>
201 <param name="sample_ploidy" type="integer" value="2" label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,--sample_ploidy" /> 192 <param name="sample_ploidy" type="integer" value="2"
193 label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,--sample_ploidy" />
202 </expand> 194 </expand>
203 </inputs> 195 </inputs>
204 <outputs> 196 <outputs>
205 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" /> 197 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" />
206 <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" /> 198 <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" />
233 <param name="indelGapOpenPenalty" value="3" /> 225 <param name="indelGapOpenPenalty" value="3" />
234 <param name="indelHaplotypeSize" value="80" /> 226 <param name="indelHaplotypeSize" value="80" />
235 <param name="doContextDependentGapPenalties" /> 227 <param name="doContextDependentGapPenalties" />
236 <!-- <param name="annotation" value="" /> 228 <!-- <param name="annotation" value="" />
237 <param name="group" value="" /> --> 229 <param name="group" value="" /> -->
238 <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" /> 230 <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" />
239 <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" /> 231 <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" />
240 <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains" /> 232 <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains" />
241 </test> 233 </test>
242 </tests> 234 </tests>
243 <help> 235 <help>
244 **What it does** 236 **What it does**