comparison realigner_target_creator.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_realigner_target_creator" name="Realigner Target Creator" version="@VERSION@.0">
  <description>for use in local realignment</description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>
  <command interpreter="python">
    gatk2_wrapper.py
    --stdout "${output_log}"
    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
    #if str( $reference_source.input_bam.metadata.bam_index ) != "None":

            #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( $rod_bind_name, -1 ) + 1
        -d "-known:${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 $analysis_param_type.analysis_param_type_selector == "advanced":
        -p '
        --minReadsAtLocus "${analysis_param_type.minReadsAtLocus}"

            <filter type="data_meta" key="dbkey" ref="input_bam" />
          </options>
        </param>
      </when>
    </conditional>
    
    <repeat name="rod_bind" title="Known Variants" help="Using data sets of known variants (-known,--known &amp;lt;known&amp;gt;)">
        <conditional name="rod_bind_type">
          <param name="rod_bind_type_selector" type="select" label="Variant 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="Variant file (VCF format)" />

              <param name="custom_rod_name" type="text" value="Unknown" label="Customer's variant file" />
              <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" />
          </when>
        </conditional>
    </repeat>
    
    <expand macro="gatk_param_type_conditional" />
    
    <expand macro="analysis_type_conditional">
        <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)" help="-window,--windowSize &amp;lt;windowSize&amp;gt;" />
        <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)" help="to disable set to &lt;= 0 or &gt; 1 (-mismatch,--mismatchFraction &amp;lt;mismatchFraction&amp;gt;)"/>
        <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)" help="-minReads,--minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
        <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
    </expand>
  </inputs>
  <outputs>
    <data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" />

          <param name="analysis_param_type_selector" value="advanced" />
          <param name="windowSize" value="10" />
          <param name="mismatchFraction" value="0.15" />
          <param name="minReadsAtLocus" value="4" />
          <param name="maxIntervalSize" value="500" />
          <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" /> 
          <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/>
      </test>
  </tests>
  <help>
**What it does**

6:35c00763cb5c

<tool id="gatk2_realigner_target_creator" name="Realigner Target Creator" version="@VERSION@.1">
  <description>for use in local realignment</description>
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <expand macro="version_command" />
  <command interpreter="python">
    gatk2_wrapper.py
    --stdout "${output_log}"
    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
    #if str( $reference_source.input_bam.metadata.bam_index ) != "None":

            #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( $rod_bind_name, -1 ) + 1
        -d "-known:${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

    $allow_n_cigar_reads
    #include source=$standard_gatk_options#
    ##start analysis specific options
    #if $analysis_param_type.analysis_param_type_selector == "advanced":
        -p '
        --minReadsAtLocus "${analysis_param_type.minReadsAtLocus}"

            <filter type="data_meta" key="dbkey" ref="input_bam" />
          </options>
        </param>
      </when>
    </conditional>

    <repeat name="rod_bind" title="Known Variants" help="Using data sets of known variants (-known,--known &amp;lt;known&amp;gt;)">
        <conditional name="rod_bind_type">
          <param name="rod_bind_type_selector" type="select" label="Variant 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="Variant file (VCF format)" />

              <param name="custom_rod_name" type="text" value="Unknown" label="Customer's variant file" />
              <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" />
          </when>
        </conditional>
    </repeat>

    <expand macro="allow_n_cigar_reads" />
    <expand macro="gatk_param_type_conditional" />

    <expand macro="analysis_type_conditional">
        <param name="windowSize" type="integer" value="10" label="Window size for calculating entropy or SNP clusters (windowSize)"
            help="-window,--windowSize &amp;lt;windowSize&amp;gt;" />
        <param name="mismatchFraction" type="float" value="0.15" label="Fraction of base qualities needing to mismatch for a position to have high entropy (mismatchFraction)"
            help="to disable set to &lt;= 0 or &gt; 1 (-mismatch,--mismatchFraction &amp;lt;mismatchFraction&amp;gt;)"/>
        <param name="minReadsAtLocus" type="integer" value="4" label="Minimum reads at a locus to enable using the entropy calculation (minReadsAtLocus)"
            help="-minReads,--minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
        <param name="maxIntervalSize" type="integer" value="500" label="Maximum interval size" help="-maxInterval,--maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
    </expand>
  </inputs>
  <outputs>
    <data format="gatk_interval" name="output_interval" label="${tool.name} on ${on_string} (GATK intervals)" />

          <param name="analysis_param_type_selector" value="advanced" />
          <param name="windowSize" value="10" />
          <param name="mismatchFraction" value="0.15" />
          <param name="minReadsAtLocus" value="4" />
          <param name="maxIntervalSize" value="500" />
          <output name="output_interval" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval" />
          <output name="output_log" file="gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains" compare="contains"/>
      </test>
  </tests>
  <help>
**What it does**