comparison variant_validate.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_validate" name="Validate Variants" version="@VERSION@.0">
  <description></description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>
  <command interpreter="python">
    gatk2_wrapper.py
   --stdout "${output_log}"
   -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
   -p '
   @JAR_PATH@
    -T "ValidateVariants"
    
    \$GATK2_SITE_OPTIONS

    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"
    #end if
    ${warn_on_errors}
    ${do_not_validate_filtered_records}
   '
    @DBSNP_OPTIONS@
   
    #include source=$standard_gatk_options#
  </command>
  <inputs>
    
    <conditional name="reference_source">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">

        <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&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>
    <expand macro="dbsnp_param" />
    
    <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/>
    <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/>
    
    <expand macro="gatk_param_type_conditional" />
    
  </inputs>
  <outputs>
    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />
  </outputs>
  <tests>

6:35c00763cb5c

<tool id="gatk2_variant_validate" name="Validate 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 "${output_log}"
   -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
   -p '
   @JAR_PATH@
    -T "ValidateVariants"

    \$GATK2_SITE_OPTIONS

    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"
    #end if
    ${warn_on_errors}
    ${do_not_validate_filtered_records}
   '
    @DBSNP_OPTIONS@

    #include source=$standard_gatk_options#
  </command>
  <inputs>

    <conditional name="reference_source">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&amp;gt;" />
        <param name="ref_file" type="select" label="Using reference genome" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;">

        <param name="input_variant" type="data" format="vcf" label="Input variant file" help="-V,--variant &amp;lt;variant&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>
    <expand macro="dbsnp_param" />

    <param name="warn_on_errors" type="boolean" checked="False" truevalue="-warnOnErrors" falsevalue="" label="instead of terminating the run at the first error, print warning messages for each error seen." help="-warnOnErrors,--warnOnErrors"/>
    <param name="do_not_validate_filtered_records" type="boolean" checked="False" truevalue="-doNotValidateFilteredRecords" falsevalue="" label="do not try to validate records that are FILTERed." help="-doNotValidateFilteredRecords,--doNotValidateFilteredRecords"/>

    <expand macro="gatk_param_type_conditional" />

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