comparison variant_combine.xml @ 6:35c00763cb5c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33

5:84584664264c

<tool id="gatk2_variant_combine" name="Combine Variants" version="@VERSION@.0">
  <description></description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>
  <command interpreter="python">
    gatk2_wrapper.py
    --stdout "${output_log}"

    #set $priority_order = []

        -R "${reference_source.ref_file.fields.path}"
    #end if
   --genotypemergeoption "${genotype_merge_option}"
   --rod_priority_list "${ ','.join( $priority_order ) }"
   '
   
    #include source=$standard_gatk_options#
    
    
    ##start analysis specific options
    #if $analysis_param_type.analysis_param_type_selector == "advanced":
        -p '
        --filteredrecordsmergetype "${analysis_param_type.filtered_records_merge_type}"
        ${analysis_param_type.print_complex_merges}
        ${analysis_param_type.filtered_are_uncalled}
        ${analysis_param_type.minimal_vcf}
        ${analysis_param_type.assume_identical_samples}
        
        #if str( $analysis_param_type.set_key ):
            --setKey "${analysis_param_type.set_key}"
        #end if
        
        --minimumN "${analysis_param_type.minimum_n}"
        '
    #end if
  </command>
  <inputs>
    
    <conditional name="reference_source">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &amp;lt;variant&amp;gt;)">
          <param name="input_variant" type="data" format="vcf" label="Input variant 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>
    
    <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption &amp;lt;genotypemergeoption&amp;gt;" >
      <option value="UNIQUIFY" />
      <option value="PRIORITIZE" selected="true"/>
      <option value="UNSORTED" />
      <option value="REQUIRE_UNIQUE" />
    </param>
    
    <expand macro="gatk_param_type_conditional" />
    
    
    <expand macro="analysis_type_conditional">
        <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;" >
          <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/>
          <option value="KEEP_IF_ALL_UNFILTERED" />
        </param>
        
        <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" />
        <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" />
        <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" />
        
        <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey &amp;lt;setKey&amp;gt;"/>
        <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" />
        <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &amp;lt;minimumN&amp;gt;"/>
        
    </expand>
    
    
  </inputs>
  <outputs>
    <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (variants)" />
    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
  </outputs>

6:35c00763cb5c

<tool id="gatk2_variant_combine" name="Combine Variants" version="@VERSION@.0">
  <description></description>
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <command interpreter="python">
    gatk2_wrapper.py
    --stdout "${output_log}"

    #set $priority_order = []

        -R "${reference_source.ref_file.fields.path}"
    #end if
   --genotypemergeoption "${genotype_merge_option}"
   --rod_priority_list "${ ','.join( $priority_order ) }"
   '

    #include source=$standard_gatk_options#

    ##start analysis specific options
    #if $analysis_param_type.analysis_param_type_selector == "advanced":
        -p '
        --filteredrecordsmergetype "${analysis_param_type.filtered_records_merge_type}"
        ${analysis_param_type.print_complex_merges}
        ${analysis_param_type.filtered_are_uncalled}
        ${analysis_param_type.minimal_vcf}
        ${analysis_param_type.assume_identical_samples}

        #if str( $analysis_param_type.set_key ):
            --setKey "${analysis_param_type.set_key}"
        #end if

        --minimumN "${analysis_param_type.minimum_n}"
        '
    #end if
  </command>
  <inputs>

    <conditional name="reference_source">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <repeat min="1" name="input_variants" title="Variants to Merge" help="Records will be prioritized in the order that you list them here (-V,--variant &amp;lt;variant&amp;gt;)">
          <param name="input_variant" type="data" format="vcf" label="Input variant 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>

    <param name="genotype_merge_option" type="select" label="How should we merge genotype records across records for samples shared across the ROD files" help="-genotypeMergeOptions,--genotypemergeoption &amp;lt;genotypemergeoption&amp;gt;" >
      <option value="UNIQUIFY" />
      <option value="PRIORITIZE" selected="true"/>
      <option value="UNSORTED" />
      <option value="REQUIRE_UNIQUE" />
    </param>

    <expand macro="gatk_param_type_conditional" />

    <expand macro="analysis_type_conditional">
        <param name="filtered_records_merge_type" type="select" label="How should we deal with records seen at the same site in the VCF, but with different FILTER fields?" help="-filteredRecordsMergeType,--filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;" >
          <option value="KEEP_IF_ANY_UNFILTERED" selected="true"/>
          <option value="KEEP_IF_ALL_UNFILTERED" />
        </param>

        <param name="print_complex_merges" checked="false" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,--printComplexMerges" />
        <param name="filtered_are_uncalled" checked="false" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotation don't appear in the combined VCF" help="-filteredAreUncalled,--filteredAreUncalled" />
        <param name="minimal_vcf" checked="false" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype INFO field" help="-minimalVCF,--minimalVCF" />

        <param name="set_key" type="text" value="" label="Key, by default set, in the INFO key=value tag emitted describing which set the combined VCF record came from." help="-setKey,--setKey &amp;lt;setKey&amp;gt;"/>
        <param name="assume_identical_samples" checked="false" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls so that one can simply perform a merge sort to combine the VCFs into one, drastically reducing the runtime." help="-assumeIdenticalSamples,--assumeIdenticalSamples" />
        <param name="minimum_n" type="integer" value="1" label="Combine variants and output site only if variant is present in at least N input files." help="-minN,--minimumN &amp;lt;minimumN&amp;gt;"/>
    </expand>

  </inputs>
  <outputs>
    <data format="vcf" name="output_variants" label="${tool.name} on ${on_string} (variants)" />
    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
  </outputs>