comparison variant_apply_recalibration.xml @ 11:0d369d08ad6e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit 344140b8df53b8b7024618bb04594607a045c03a

10:5db8d6815cf3

<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" version="@VERSION@.0">
  <description></description>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>
  <command interpreter="python">
    gatk2_wrapper.py
    --stdout "${output_log}"
    #for $var_count, $variant in enumerate( $reference_source.variants ):
        -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"

    #end if
    --recal_file "${reference_source.input_recal}"
    --tranches_file "${reference_source.input_tranches}"
    --out "${output_variants}"
   '
    
    #include source=$standard_gatk_options#
    
    ##start analysis specific options
    -p '
    --mode "${mode}"
    
    #for $ignore_filter in $ignore_filters:
        #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
        #if $ignore_filter_name == "custom":
          #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
        #end if

        <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
        <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&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="gatk_param_type_conditional" />
    
        <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
          <option value="SNP" selected="True">SNP</option>
          <option value="INDEL">INDEL</option>
          <option value="BOTH">BOTH</option>
        </param>

11:0d369d08ad6e

<tool id="gatk2_variant_apply_recalibration" name="Apply Variant Recalibration" 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}"
    #for $var_count, $variant in enumerate( $reference_source.variants ):
        -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"

    #end if
    --recal_file "${reference_source.input_recal}"
    --tranches_file "${reference_source.input_tranches}"
    --out "${output_variants}"
   '

    #include source=$standard_gatk_options#

    ##start analysis specific options
    -p '
    --mode "${mode}"

    #for $ignore_filter in $ignore_filters:
        #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.ignore_filter_type_selector )
        #if $ignore_filter_name == "custom":
          #set $ignore_filter_name = str( $ignore_filter.ignore_filter_type.filter_name )
        #end if

        <param name="input_recal" type="data" format="gatk_recal" label="Variant Recalibration file" help="-recalFile,--recal_file &amp;lt;recal_file&amp;gt;" />
        <param name="input_tranches" type="data" format="gatk_tranche" label="Variant Tranches file" help="-tranchesFile,--tranches_file &amp;lt;tranches_file&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="gatk_param_type_conditional" />

        <param name="mode" type="select" label="Recalibration mode" help="-mode,--mode &amp;lt;mode&amp;gt;">
          <option value="SNP" selected="True">SNP</option>
          <option value="INDEL">INDEL</option>
          <option value="BOTH">BOTH</option>
        </param>