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diff variant_eval.xml @ 15:01ff8dd37d4d draft default tip

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author lz_hust
date Sat, 01 Jun 2019 07:20:41 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_eval.xml	Sat Jun 01 07:20:41 2019 -0400
@@ -0,0 +1,276 @@
+<tool id="gatk2_variant_eval" name="Eval Variants" version="@VERSION@.1">
+  <description></description>
+  <macros>
+    <import>gatk2_macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
+  <command interpreter="python">
+   #from binascii import hexlify
+
+    gatk2_wrapper.py
+   --stdout "${output_log}"
+    #for $var_count, $variant in enumerate( $reference_source.input_variants ):
+        -d "--eval:input_${var_count},%(file_type)s" "${variant}" "${variant.ext}" "input_variants_${var_count}"
+    #end for
+    -p '
+    @JAR_PATH@
+    -T "VariantEval"
+    --out "${output_report}"
+    \$GATK2_SITE_OPTIONS
+
+    @THREADS@
+
+    #if $reference_source.reference_source_selector != "history":
+        -R "${reference_source.ref_file.fields.path}"
+    #end if
+   '
+
+    #for $rod_binding in $comp_rod_bind:
+        -d "--comp:${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}"
+        #if str( $rod_binding.comp_known_names ):
+            -p '--known_names "${rod_binding.comp_rod_name}"'
+        #end if
+    #end for
+
+    #if $dbsnp_rod_bind_type.dbsnp_rod_bind_type_selector == 'set_dbsnp'
+        -d "--dbsnp:${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}"
+        #if $dbsnp_rod_bind_type.dbsnp_known_names
+            -p '--known_names "${dbsnp_rod_bind_type.dbsnp_rod_name}"'
+        #end if
+    #end if
+
+    #include source=$standard_gatk_options#
+
+    ##start analysis specific options
+    #if $analysis_param_type.analysis_param_type_selector == "advanced":
+        #for $stratification in $analysis_param_type.stratifications:
+            #set $select_string = "--select_exps '%s' --select_names '%s'" % ( str( $stratification.select_exps ), str( $stratification.select_name )  )
+            -o '${ hexlify( $select_string ) }'
+        #end for
+        -p '
+
+        #for $sample in $analysis_param_type.samples:
+            --sample "${sample.sample}"
+        #end for
+
+        #if str( $analysis_param_type.stratification_modules ) != "None":
+            #for $stratification_module in str( $analysis_param_type.stratification_modules).split( ',' ):
+                --stratificationModule "${stratification_module}"
+            #end for
+        #end if
+
+        ${analysis_param_type.do_not_use_all_standard_stratifications}
+
+        #for $variant_type in $analysis_param_type.only_variants_of_type:
+            --onlyVariantsOfType "${variant_type.variant_type}"
+        #end for
+
+        #if str( $analysis_param_type.eval_modules ) != "None":
+            #for $eval_module in str( $analysis_param_type.eval_modules).split( ',' ):
+                --evalModule "${eval_module}"
+            #end for
+        #end if
+
+        ${analysis_param_type.do_not_use_all_standard_modules}
+
+        #if str( $analysis_param_type.num_samples ) != "0":
+            --numSamples "${analysis_param_type.num_samples}"
+        #end if
+
+        --minPhaseQuality "${analysis_param_type.min_phase_quality}"
+
+        --mendelianViolationQualThreshold "${analysis_param_type.mendelian_violation_qual_threshold}"
+
+        #if str( $analysis_param_type.ancestral_alignments ) != "None":
+            --ancestralAlignments "${analysis_param_type.ancestral_alignments}"
+        #end if
+        '
+        #if str( $analysis_param_type.known_cnvs ) != "None":
+            -d "--knownCNVs" "${analysis_param_type.known_cnvs}" "${analysis_param_type.known_cnvs.ext}" "input_known_cnvs"
+        #end if
+
+        #if str( $analysis_param_type.strat_intervals ) != "None":
+            -d "--stratIntervals" "${analysis_param_type.strat_intervals}" "${analysis_param_type.strat_intervals.ext}" "input_strat_intervals"
+        #end if
+    #end if
+  </command>
+  <inputs>
+
+    <conditional name="reference_source">
+      <expand macro="reference_source_selector_param" />
+      <when value="cached">
+        <expand macro="input_variants" help="-eval,--eval &amp;lt;eval&amp;gt;"/>
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">
+          <options from_data_table="gatk2_picard_indexes">
+            <!-- <filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/> -->
+          </options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+        </param>
+      </when>
+      <when value="history"> <!-- FIX ME!!!! -->
+        <expand macro="input_variants" help="-eval,--eval &amp;lt;eval&amp;gt;" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
+      </when>
+    </conditional>
+
+    <repeat name="comp_rod_bind" title="Comparison Reference-Ordered Data (ROD) file" help="-comp,--comp &amp;lt;comp&amp;gt;">
+      <param name="comp_input_rod" type="data" format="vcf" label="Comparison ROD file" />
+      <param name="comp_rod_name" type="text" value="" label="Comparison ROD name">
+          <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
+      </param>
+      <param name="comp_known_names" type="boolean" label="Use comparison ROD file as known_names" help="-knownName,--known_names &amp;lt;known_names&amp;gt;"/>
+    </repeat>
+    <conditional name="dbsnp_rod_bind_type">
+      <param name="dbsnp_rod_bind_type_selector" type="select" label="Provide a dbSNP Reference-Ordered Data (ROD) file" help="-D,--dbsnp &amp;lt;dbsnp&amp;gt;">
+        <option value="set_dbsnp" selected="True">Set dbSNP</option>
+        <option value="exclude_dbsnp">Don't set dbSNP</option>
+      </param>
+      <when value="exclude_dbsnp" />
+      <when value="set_dbsnp">
+        <param name="dbsnp_input_rod" type="data" format="vcf" label="dbSNP ROD file" />
+        <param name="dbsnp_rod_name" type="text" value="dbsnp" label="dbsnp ROD name">
+          <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator>
+        </param>
+        <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;" />
+      </when>
+    </conditional>
+
+    <expand macro="gatk_param_type_conditional" />
+
+    <expand macro="analysis_type_conditional">
+        <repeat name="stratifications" title="Stratification">
+          <param name="select_exps" value="" type="text" label="Stratification Expression" help="-select,--select_exps &amp;lt;select_exps&amp;gt;">
+            <sanitizer>
+              <valid initial="string.printable">
+               <remove value="&apos;"/>
+             </valid>
+              <mapping initial="none"/>
+            </sanitizer>
+          </param>
+          <param name="select_name" value="" type="text" label="Name" help="-selectName,--select_names &amp;lt;select_names&amp;gt;"/>
+        </repeat>
+
+        <repeat name="samples" title="Sample" help="-sn,--sample &amp;lt;sample&amp;gt;">
+          <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"/>
+        </repeat>
+
+        <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;" >
+          <option value="AlleleCount" />
+          <option value="AlleleFrequency" />
+          <option value="CompRod" />
+          <option value="Contig" />
+          <option value="CpG" />
+          <option value="Degeneracy" />
+          <option value="EvalRod" />
+          <option value="Filter" />
+          <option value="FunctionalClass" />
+          <option value="IndelSize" />
+          <option value="IntervalStratification" />
+          <option value="JexlExpression" />
+          <option value="Novelty" />
+          <option value="OneBPIndel" />
+          <option value="Sample" />
+          <option value="SnpEffPositionModifier" />
+          <option value="TandemRepeat" />
+          <option value="VariantType" />
+        </param>
+        <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" />
+
+        <repeat name="only_variants_of_type" title="only Variants Of Type" help="--onlyVariantsOfType">
+          <param name="variant_type" type="text" value="" label="only variants of these types will be considered during the evaluation"/>
+        </repeat>
+
+        <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;" >
+          <option value="CompOverlap" />
+          <option value="CountVariants" />
+          <option value="IndelLengthHistogram" />
+          <option value="IndelSummary" />
+          <option value="MendelianViolationEvaluator" />
+          <option value="MultiallelicSummary" />
+          <option value="PrintMissingComp" />
+          <option value="ThetaVariantEvaluator" />
+          <option value="TiTvVariantEvaluator" />
+          <option value="ValidationReport" />
+          <option value="VariantSummary" />
+        </param>
+        <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" />
+
+        <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;"/>
+        <param name="min_phase_quality" type="float" label="Minimum phasing quality " value="10.0" help="-mpq,--minPhaseQuality &amp;lt;minPhaseQuality&amp;gt;"/>
+        <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;"/>
+        <param name="ancestral_alignments" type="data" format="fasta" optional="True" label="Fasta file with ancestral alleles" help="-aa,--ancestralAlignments &amp;lt;ancestralAlignments&amp;gt;" />
+        <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;" />
+        <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;" />
+    </expand>
+
+  </inputs>
+  <outputs>
+    <data format="gatk_report" name="output_report" label="${tool.name} on ${on_string} (report)" />
+    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
+  </outputs>
+  <tests>
+      <test>
+          <param name="reference_source_selector" value="history" />
+          <param name="ref_file" value="phiX.fasta" ftype="fasta" />
+          <param name="input_variant" value="gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf" ftype="vcf" />
+          <param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" />
+          <param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" />
+          <param name="dbsnp_rod_name" value="dbsnp" />
+          <param name="dbsnp_known_names" value="True"/>
+          <param name="comp_rod_bind" value="0" />
+          <param name="gatk_param_type_selector" value="basic" />
+          <param name="analysis_param_type_selector" value="basic" />
+          <output name="output_report" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report" />
+          <output name="output_log" file="gatk/gatk_variant_eval/gatk_variant_eval_out_1.log.contains" compare="contains" />
+      </test>
+  </tests>
+  <help>
+**What it does**
+
+General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more)
+
+For more information on using the VariantEval module, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_varianteval_VariantEval.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: VariantEval accepts variant files as input.
+
+
+**Outputs**
+
+The output is a table of variant evaluation.
+
+
+Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.
+
+-------
+
+**Settings**::
+
+ out                                   An output file presented to the walker. Will overwrite contents if file exists.
+ list                                  List the available eval modules and exit
+ select_exps                           One or more stratifications to use when evaluating the data
+ select_names                          Names to use for the list of stratifications (must be a 1-to-1 mapping)
+ sample                                Derive eval and comp contexts using only these sample genotypes, when genotypes are available in the original context
+ known_names                           Name of ROD bindings containing variant sites that should be treated as known when splitting eval rods into known and novel subsets
+ stratificationModule                  One or more specific stratification modules to apply to the eval track(s) (in addition to the standard stratifications, unless -noS is specified)
+ doNotUseAllStandardStratifications    Do not use the standard stratification modules by default (instead, only those that are specified with the -S option)
+ onlyVariantsOfType                    If provided, only variants of these types will be considered during the evaluation, in
+ evalModule                            One or more specific eval modules to apply to the eval track(s) (in addition to the standard modules, unless -noE is specified)
+ doNotUseAllStandardModules            Do not use the standard modules by default (instead, only those that are specified with the -E option)
+ numSamples                            Number of samples (used if no samples are available in the VCF file
+ minPhaseQuality                       Minimum phasing quality
+ mendelianViolationQualThreshold       Minimum genotype QUAL score for each trio member required to accept a site as a violation
+ ancestralAlignments                   Fasta file with ancestral alleles
+
+@CITATION_SECTION@
+  </help>
+  <expand macro="citations" />
+</tool>