diff unified_genotyper.xml @ 0:340633249b3d draft

Uploaded
author bgruening
date Mon, 02 Dec 2013 06:18:36 -0500
parents
children 8bcc13094767
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+++ b/unified_genotyper.xml	Mon Dec 02 06:18:36 2013 -0500
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+<tool id="gatk2_unified_genotyper" name="Unified Genotyper" version="0.0.7">
+  <description>SNP and indel caller</description>
+  <expand macro="requirements" />
+  <macros>
+    <import>gatk2_macros.xml</import>
+  </macros>
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    #for $i, $input_bam in enumerate( $reference_source.input_bams ):
+        -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
+        #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
+            -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
+        #end if
+    #end for
+    -p '
+    @JAR_PATH@
+    -T "UnifiedGenotyper"
+    @THREADS@
+    --out "${output_vcf}"
+    --metrics_file "${output_metrics}"
+    \$GATK2_SITE_OPTIONS
+
+    ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
+    --num_cpu_threads_per_data_thread 6
+
+    #if $reference_source.reference_source_selector != "history":
+        -R "${reference_source.ref_file.fields.path}"
+    #end if
+    --genotype_likelihoods_model "${genotype_likelihoods_model}"
+    --standard_min_confidence_threshold_for_calling "${standard_min_confidence_threshold_for_calling}"
+    --standard_min_confidence_threshold_for_emitting "${standard_min_confidence_threshold_for_emitting}"
+   '
+    #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
+        #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( $rod_bind_name, -1 ) + 1
+        -d "--dbsnp:${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[$rod_bind_name]}"
+    #end for
+   
+    #include source=$standard_gatk_options#
+    ##start analysis specific options
+    #if $analysis_param_type.analysis_param_type_selector == "advanced":
+        -p '
+        --p_nonref_model "${analysis_param_type.p_nonref_model}"
+        --heterozygosity "${analysis_param_type.heterozygosity}"
+        --pcr_error_rate "${analysis_param_type.pcr_error_rate}"
+        --genotyping_mode "${analysis_param_type.genotyping_mode_type.genotyping_mode}"
+        #if str( $analysis_param_type.genotyping_mode_type.genotyping_mode ) == 'GENOTYPE_GIVEN_ALLELES':
+            --alleles "${analysis_param_type.genotyping_mode_type.input_alleles_rod}"
+        #end if
+        --output_mode "${analysis_param_type.output_mode}"
+        ${analysis_param_type.compute_SLOD}
+        --min_base_quality_score "${analysis_param_type.min_base_quality_score}"
+        --max_deletion_fraction "${analysis_param_type.max_deletion_fraction}"
+        --max_alternate_alleles "${analysis_param_type.max_alternate_alleles}"
+        --min_indel_count_for_genotyping "${analysis_param_type.min_indel_count_for_genotyping}"
+        --indel_heterozygosity "${analysis_param_type.indel_heterozygosity}"
+        --indelGapContinuationPenalty "${analysis_param_type.indelGapContinuationPenalty}"
+        --indelGapOpenPenalty "${analysis_param_type.indelGapOpenPenalty}"
+        --indelHaplotypeSize "${analysis_param_type.indelHaplotypeSize}"
+        ${analysis_param_type.doContextDependentGapPenalties}
+        #if str( $analysis_param_type.annotation ) != "None":
+            #for $annotation in str( $analysis_param_type.annotation.fields.gatk_value ).split( ','):
+                --annotation "${annotation}"
+            #end for
+        #end if
+        #for $additional_annotation in $analysis_param_type.additional_annotations:
+            --annotation "${additional_annotation.additional_annotation_name}"
+        #end for
+        #if str( $analysis_param_type.group ) != "None":
+            #for $group in str( $analysis_param_type.group ).split( ','):
+                --group "${group}"
+            #end for
+        #end if
+        #if str( $analysis_param_type.exclude_annotations ) != "None":
+            #for $annotation in str( $analysis_param_type.exclude_annotations.fields.gatk_value ).split( ','):
+                --excludeAnnotation "${annotation}"
+            #end for
+        #end if
+        ${analysis_param_type.multiallelic}
+        #if str( $analysis_param_type.sample_ploidy ) != '':
+          --sample_ploidy "$analysis_param_type.sample_ploidy"
+        #end if
+        '
+##        #if str( $analysis_param_type.snpEff_rod_bind_type.snpEff_rod_bind_type_selector ) == 'set_snpEff':
+##            -p '--annotation "SnpEff"'
+##            -d "--snpEffFile:${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name},%(file_type)s" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod}" "${analysis_param_type.snpEff_rod_bind_type.snpEff_input_rod.ext}" "input_snpEff_${analysis_param_type.snpEff_rod_bind_type.snpEff_rod_name}"
+##        #else:
+##            -p '--excludeAnnotation "SnpEff"'
+##        #end if
+    #end if
+  </command>
+  <inputs>
+    <conditional name="reference_source">
+      <expand macro="reference_source_selector_param" />
+      <when value="cached">
+        <repeat name="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
+            <param name="input_bam" type="data" format="bam" label="BAM file">
+              <validator type="unspecified_build" />
+              <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 -->
+            </param>
+        </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="input_bam" column="dbkey"/> does not yet work in a repeat...--> 
+          </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="input_bams" title="BAM file" min="1" help="-I,--input_file &amp;lt;input_file&amp;gt;">
+            <param name="input_bam" type="data" format="bam" label="BAM file" >
+            </param>
+        </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="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
+        <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="snps">SNPs</option>
+            <option value="indels">INDELs</option>
+            <option value="custom">Custom</option>
+          </param>
+          <when value="dbsnp">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+          </when>
+          <when value="snps">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+          </when>
+          <when value="indels">
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+          </when>
+          <when value="custom">
+              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
+              <param name="input_rod" type="data" format="vcf" label="ROD file" />
+          </when>
+        </conditional>
+    </repeat>
+    
+    <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;">
+      <option value="BOTH" selected="True">BOTH</option>
+      <option value="SNP">SNP</option>
+      <option value="INDEL">INDEL</option>
+    </param>
+    
+    <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;" />
+    <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;" />
+
+    
+    <expand macro="gatk_param_type_conditional" />
+    
+    <expand macro="analysis_type_conditional">
+        <param name="p_nonref_model" type="select" label="Non-reference probability calculation model to employ" help="-pnrm,--p_nonref_model &amp;lt;p_nonref_model&amp;gt;">
+          <option value="EXACT_GENERAL_PLOIDY" selected="True">EXACT_GENERAL_PLOIDY (supports any sample ploidy)</option>
+          <option value="EXACT_REFERENCE">EXACT_REFERENCE (multi-allelic EXACT model.  Extremely slow for many alternate alleles)</option>
+        </param>
+        <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;" />
+        <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;" />
+        <conditional name="genotyping_mode_type">
+          <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;">
+            <option value="DISCOVERY" selected="True">DISCOVERY</option>
+            <option value="GENOTYPE_GIVEN_ALLELES">GENOTYPE_GIVEN_ALLELES</option>
+          </param>
+          <when value="DISCOVERY">
+            <!-- Do nothing here -->
+          </when>
+          <when value="GENOTYPE_GIVEN_ALLELES">
+            <param name="input_alleles_rod" type="data" format="vcf" label="Alleles ROD file" help="-alleles,--alleles &amp;lt;alleles&amp;gt;" />
+          </when>
+        </conditional>
+        <param name="output_mode" type="select" label="Should we output confident genotypes (i.e. including ref calls) or just the variants?" help="-out_mode,--output_mode &amp;lt;output_mode&amp;gt;">
+          <option value="EMIT_VARIANTS_ONLY" selected="True">EMIT_VARIANTS_ONLY</option>
+          <option value="EMIT_ALL_CONFIDENT_SITES">EMIT_ALL_CONFIDENT_SITES</option>
+          <option value="EMIT_ALL_SITES">EMIT_ALL_SITES</option>
+        </param>
+        <param name="compute_SLOD" type="boolean" truevalue="--computeSLOD" falsevalue="" label="Compute the SLOD" help="--computeSLOD" />
+        <param name="min_base_quality_score" type="integer" value="17" label="Minimum base quality required to consider a base for calling" help="-mbq,--min_base_quality_score &amp;lt;min_base_quality_score&amp;gt;" />
+        <param name="max_deletion_fraction" type="float" value="0.05" label="Maximum fraction of reads with deletions spanning this locus for it to be callable" help="to disable, set to &lt; 0 or &gt; 1 (-deletions,--max_deletion_fraction &amp;lt;max_deletion_fraction&amp;gt;)" />
+        <param name="max_alternate_alleles" type="integer" value="6" label="Maximum number of alternate alleles to genotype" help="-maxAlleles,--max_alternate_alleles &amp;lt;max_alternate_alleles&amp;gt;" />
+        <param name="min_indel_count_for_genotyping" type="integer" value="5" label="Minimum number of consensus indels required to trigger genotyping run" help="-minIndelCnt,--min_indel_count_for_genotyping &amp;lt;min_indel_count_for_genotyping&amp;gt;" />
+        <param name="indel_heterozygosity" type="float" value="0.000125" label="Heterozygosity for indel calling" help="1.0/8000==0.000125 (-indelHeterozygosity,--indel_heterozygosity &amp;lt;indel_heterozygosity&amp;gt;)"/>
+        <param name="indelGapContinuationPenalty" type="integer" value="10" label="Indel gap continuation penalty" help="--indelGapContinuationPenalty">
+          <help>Indel gap continuation penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help>
+          <validator type="in_range" message="value between 0 and 255" min="0" max="255"/> 
+        </param>
+        <param name="indelGapOpenPenalty" type="integer" value="45" label="Indel gap open penalty" help="--indelGapOpenPenalty" >
+          <help>Indel gap open penalty, as Phred-scaled probability. I.e., 30 => 10^-30/10.</help>
+          <validator type="in_range" message="value between 0 and 255" min="0" max="255"/> 
+        </param>
+        <!-- indelHaplotypeSize - Gone in GATK 2.4? -->
+        <param name="indelHaplotypeSize" type="integer" value="80" label="Indel haplotype size" help="--indelHaplotypeSize" />
+        <param name="doContextDependentGapPenalties" type="boolean" truevalue="--doContextDependentGapPenalties" falsevalue="" label="Vary gap penalties by context" help="--doContextDependentGapPenalties" />
+        <param name="annotation" type="select" multiple="True" display="checkboxes" label="Annotation Types" help="-A,--annotation &amp;lt;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="UnifiedGenotyper" column="tools_valid_for"/>
+          </options>
+        </param>
+        <repeat name="additional_annotations" title="Additional annotation" help="-A,--annotation &amp;lt;annotation&amp;gt;">
+          <param name="additional_annotation_name" type="text" value="" label="Annotation name" />
+        </repeat>
+<!--
+        <conditional name="snpEff_rod_bind_type">
+          <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file">
+            <option value="set_snpEff">Set snpEff</option>
+            <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
+          </param>
+          <when value="exclude_snpEff">
+          </when>
+          <when value="set_snpEff">
+            <param name="snpEff_input_rod" type="data" format="vcf" label="ROD file" />
+            <param name="snpEff_rod_name" type="hidden" value="snpEff" label="ROD Name"/>
+          </when>
+        </conditional>
+-->
+        <param name="group" type="select" multiple="True" display="checkboxes" label="Annotation Interfaces/Groups" help="-G,--group &amp;lt;group&amp;gt;">
+            <option value="RodRequiringAnnotation">RodRequiringAnnotation</option>
+            <option value="Standard">Standard</option>
+            <option value="Experimental">Experimental</option>
+            <option value="WorkInProgress">WorkInProgress</option>
+            <option value="RankSumTest">RankSumTest</option>
+            <!-- <option value="none">none</option> -->
+        </param>
+    <!--     <param name="family_string" type="text" value="" label="Family String"/> -->
+        <param name="exclude_annotations" type="select" multiple="True" display="checkboxes" label="Annotations to exclude" help="-XA,--excludeAnnotation &amp;lt;excludeAnnotation&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="UnifiedGenotyper" column="tools_valid_for"/>
+          </options>
+        </param>
+        <param name="multiallelic" type="boolean" truevalue="--multiallelic" falsevalue="" label="Allow the discovery of multiple alleles (SNPs only)" help="--multiallelic" />
+    </expand>
+  </inputs>
+  <outputs>
+    <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (VCF)" />
+    <data format="txt" name="output_metrics" label="${tool.name} on ${on_string} (metrics)" />
+    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+  </outputs>
+  <trackster_conf/>
+  <tests>
+      <test>
+          <param name="reference_source_selector" value="history" />
+          <param name="ref_file" value="phiX.fasta" ftype="fasta" />
+          <param name="input_bam" value="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" />
+          <param name="rod_bind_type_selector" value="dbsnp" />
+          <param name="input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
+          <param name="standard_min_confidence_threshold_for_calling" value="0" />
+          <param name="standard_min_confidence_threshold_for_emitting" value="4" />
+          <param name="gatk_param_type_selector" value="basic" />
+          <param name="analysis_param_type_selector" value="advanced" />
+          <param name="genotype_likelihoods_model" value="BOTH" />
+          <param name="p_nonref_model" value="EXACT" />
+          <param name="heterozygosity" value="0.001" />
+          <param name="pcr_error_rate" value="0.0001" />
+          <param name="genotyping_mode" value="DISCOVERY" />
+          <param name="output_mode" value="EMIT_ALL_CONFIDENT_SITES" />
+          <param name="compute_SLOD" />
+          <param name="min_base_quality_score" value="17" />
+          <param name="max_deletion_fraction" value="-1" />
+          <param name="min_indel_count_for_genotyping" value="2" />
+          <param name="indel_heterozygosity" value="0.000125" />
+          <param name="indelGapContinuationPenalty" value="10" />
+          <param name="indelGapOpenPenalty" value="3" />
+          <param name="indelHaplotypeSize" value="80" />
+          <param name="doContextDependentGapPenalties" />
+          <!-- <param name="annotation" value="" />
+          <param name="group" value="" /> -->
+          <output name="output_vcf" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf" lines_diff="4" /> 
+          <output name="output_metrics" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics" /> 
+          <output name="output_log" file="gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains" compare="contains" />
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+A variant caller which unifies the approaches of several disparate callers.  Works for single-sample and multi-sample data.  The user can choose from several different incorporated calculation models.
+
+For more information on the GATK Unified Genotyper, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html&gt;`_.
+
+To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
+
+If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
+
+------
+
+**Inputs**
+
+GenomeAnalysisTK: UnifiedGenotyper accepts an aligned BAM input file.
+
+
+**Outputs**
+
+The output is in VCF format.
+
+
+Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
+
+-------
+
+**Settings**::
+
+ genotype_likelihoods_model                        Genotype likelihoods calculation model to employ -- BOTH is the default option, while INDEL is also available for calling indels and SNP is available for calling SNPs only (SNP|INDEL|BOTH)
+ p_nonref_model                                    Non-reference probability calculation model to employ -- EXACT_GENERAL_PLOIDY is the default option, while EXACT_REFERENCE is also available. (EXACT_INDEPENDENT,EXACT_REFERENCE,EXACT_ORIGINAL,EXACT_GENERAL_PLOIDY)
+ heterozygosity                                    Heterozygosity value used to compute prior likelihoods for any locus
+ pcr_error_rate                                    The PCR error rate to be used for computing fragment-based likelihoods
+ genotyping_mode                                   Should we output confident genotypes (i.e. including ref calls) or just the variants? (DISCOVERY|GENOTYPE_GIVEN_ALLELES)
+ output_mode                                       Should we output confident genotypes (i.e. including ref calls) or just the variants? (EMIT_VARIANTS_ONLY|EMIT_ALL_CONFIDENT_SITES|EMIT_ALL_SITES)
+ standard_min_confidence_threshold_for_calling     The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called
+ standard_min_confidence_threshold_for_emitting    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)
+ noSLOD                                            If provided, we will not calculate the SLOD
+ min_base_quality_score                            Minimum base quality required to consider a base for calling
+ max_deletion_fraction                             Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to &lt; 0 or &gt; 1; default:0.05]
+ min_indel_count_for_genotyping                    Minimum number of consensus indels required to trigger genotyping run
+ indel_heterozygosity                              Heterozygosity for indel calling
+ indelGapContinuationPenalty                       Indel gap continuation penalty
+ indelGapOpenPenalty                               Indel gap open penalty
+ indelHaplotypeSize                                Indel haplotype size
+ doContextDependentGapPenalties                    Vary gap penalties by context
+ indel_recal_file                                  Filename for the input covariates table recalibration .csv file - EXPERIMENTAL, DO NO USE
+ indelDebug                                        Output indel debug info
+ out                                               File to which variants should be written
+ annotation                                        One or more specific annotations to apply to variant calls
+ group                                             One or more classes/groups of annotations to apply to variant calls
+
+@CITATION_SECTION@
+  </help>
+</tool>