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comparison haplotype_caller.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_haplotype_caller" name="Haplotype Caller" version="@VERSION@.0"> 1 <tool id="gatk2_haplotype_caller" name="Haplotype Caller" version="@VERSION@.2">
2 <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</description> 2 <description>Call SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region</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_${i}" ##hardcode galaxy ext type as bam_index
14 #end if
15 #end for
16 -p ' 12 -p '
17 @JAR_PATH@ 13 @JAR_PATH@
18 -T "HaplotypeCaller" 14 -T "HaplotypeCaller"
19 -o "${output_vcf}" 15 -o "${output_vcf}"
20 16
28 #if str($input_recal) != 'None': 24 #if str($input_recal) != 'None':
29 --BQSR "${input_recal}" 25 --BQSR "${input_recal}"
30 #end if 26 #end if
31 ' 27 '
32 @DBSNP_OPTIONS@ 28 @DBSNP_OPTIONS@
29 $allow_n_cigar_reads
33 #include source=$standard_gatk_options# 30 #include source=$standard_gatk_options#
34 31
35 ##start analysis specific options 32 ##start analysis specific options
36 #if $analysis_param_type.analysis_param_type_selector == "advanced": 33 #if $analysis_param_type.analysis_param_type_selector == "advanced":
37 -p ' 34 -p '
38 #if $analysis_param_type.heterozygosity.__str__.strip() != '': 35 #if $analysis_param_type.heterozygosity.__str__.strip() != '':
39 --heterozygosity $analysis_param_type.heterozygosity 36 --heterozygosity $analysis_param_type.heterozygosity
51 --activeRegionIn "$analysis_param_type.activeRegionIn" 48 --activeRegionIn "$analysis_param_type.activeRegionIn"
52 #end if 49 #end if
53 #if str($analysis_param_type.comp) != 'None': 50 #if str($analysis_param_type.comp) != 'None':
54 --comp "$analysis_param_type.comp" 51 --comp "$analysis_param_type.comp"
55 #end if 52 #end if
56 ## 53 ##
57 #if str( $analysis_param_type.annotation ) != "None": 54 #if str( $analysis_param_type.annotation ) != "None":
58 #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','): 55 #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','):
59 --annotation "${annotation}" 56 --annotation "${annotation}"
60 #end for 57 #end for
61 #end if 58 #end if
115 <inputs> 112 <inputs>
116 <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="The input covariates table file which enables on-the-fly base quality score recalibration. Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool. Please be aware that one should only run recalibration with the covariates file created on the same input bam(s) (-BQSR,--BQSR &amp;lt;recal_file&amp;gt;)" /> 113 <param name="input_recal" type="data" format="gatk_report" optional="true" label="Covariates table recalibration file" help="The input covariates table file which enables on-the-fly base quality score recalibration. Enables on-the-fly recalibrate of base qualities. The covariates tables are produced by the BaseQualityScoreRecalibrator tool. Please be aware that one should only run recalibration with the covariates file created on the same input bam(s) (-BQSR,--BQSR &amp;lt;recal_file&amp;gt;)" />
117 <conditional name="reference_source"> 114 <conditional name="reference_source">
118 <expand macro="reference_source_selector_param" /> 115 <expand macro="reference_source_selector_param" />
119 <when value="cached"> 116 <when value="cached">
120 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;"> 117 <expand macro="input_bams_cached" />
121 <param name="input_bam" type="data" format="bam" label="BAM file">
122 <validator type="unspecified_build" />
123 <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 -->
124 </param>
125 </repeat>
126 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" > 118 <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
127 <options from_data_table="gatk2_picard_indexes"> 119 <options from_data_table="gatk2_picard_indexes">
128 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...--> 120 <!-- <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/> does not yet work in a repeat...-->
129 </options> 121 </options>
130 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> 122 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
131 </param> 123 </param>
132 </when> 124 </when>
133 <when value="history"> 125 <when value="history">
134 <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;"> 126 <expand macro="input_bams_history" />
135 <param name="input_bam" type="data" format="bam" label="BAM file" />
136 </repeat>
137 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" /> 127 <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
138 </when> 128 </when>
139 </conditional> 129 </conditional>
140 <expand macro="dbsnp_param" /> 130 <expand macro="dbsnp_param" />
141 131
132 <expand macro="allow_n_cigar_reads" />
142 <expand macro="gatk_param_type_conditional" /> 133 <expand macro="gatk_param_type_conditional" />
143 134
144 <conditional name="analysis_param_type"> 135 <conditional name="analysis_param_type">
145 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options"> 136 <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
146 <option value="basic" selected="True">Basic</option> 137 <option value="basic" selected="True">Basic</option>
211 </when> 202 </when>
212 <when value="GENOTYPE_GIVEN_ALLELES"> 203 <when value="GENOTYPE_GIVEN_ALLELES">
213 <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &amp;lt;alleles&amp;gt;" /> 204 <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &amp;lt;alleles&amp;gt;" />
214 </when> 205 </when>
215 </conditional> 206 </conditional>
216
217
218 <param name="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph File to which debug assembly graph information should be written"/> 207 <param name="graphOutput" type="boolean" checked="False" truevalue="" falsevalue="" label="graphOutput" help="--graphOutput / -graph File to which debug assembly graph information should be written"/>
219 <param name="heterozygosity" type="float" value="0.0010" optional="true" label="heterozygosity" help="--heterozygosity / -hets Heterozygosity value used to compute prior likelihoods for any locus"/> 208 <param name="heterozygosity" type="float" value="0.0010" optional="true" label="heterozygosity" help="--heterozygosity / -hets Heterozygosity value used to compute prior likelihoods for any locus"/>
220 <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning The minimum allowed pruning factor in assembly graph. Paths with &gt;= X supporting kmers are pruned from the graph"> 209 <param name="minPruning" type="integer" value="1" optional="true" label="minPruning" help="--minPruning / -minPruning The minimum allowed pruning factor in assembly graph. Paths with &gt;= X supporting kmers are pruned from the graph">
221 <validator type="in_range" message="value between 0 and 127" min="0" max="127"/> 210 <validator type="in_range" message="value between 0 and 127" min="0" max="127"/>
222 </param> 211 </param>
252 </data> 241 </data>
253 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> 242 <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
254 </outputs> 243 </outputs>
255 <tests> 244 <tests>
256 <test> 245 <test>
257 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> 246 <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" />
258 <param name="reference_source_selector" value="history" /> 247 <param name="reference_source_selector" value="history" />
259 <param name="ref_file" value="phiX.fasta" ftype="fasta" /> 248 <param name="ref_file" value="phiX.fasta" ftype="fasta" />
260 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" /> 249 <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
261 <param name="gatk_param_type_selector" value="basic" /> 250 <param name="gatk_param_type_selector" value="basic" />
262 <param name="analysis_param_type_selector" value="basic" /> 251 <param name="analysis_param_type_selector" value="basic" />