comparison indel_realigner.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_indel_realigner" name="Indel Realigner" version="@VERSION@.0">
  <description>- perform 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":

        -R "${reference_source.ref_file.fields.path}"
    #end if
   -LOD "${lod_threshold}"
    ${knowns_only}
   '
   
    #set $rod_binding_names = dict()
    #for $rod_binding in $rod_bind:
        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
            #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
        #else
            #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=$standard_gatk_options#
    ##start analysis specific options
    -d "-targetIntervals" "${target_intervals}" "${target_intervals.ext}" "gatk_target_intervals"
    -p '
    --disable_bam_indexing

        ${analysis_param_type.no_original_alignment_tags}
        '
    #end if
  </command>
  <inputs>
    
    <conditional name="reference_source">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
          <validator type="unspecified_build" />

          </when>
        </conditional>
    </repeat>
    <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" help="-LOD,--LODThresholdForCleaning &amp;lt;LODThresholdForCleaning&amp;gt;" />
    <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs" help="-knownsOnly"/>
    
    <expand macro="gatk_param_type_conditional" />
    
    <expand macro="analysis_type_conditional">
        
        <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" help="-entropy,--entropyThreshold &amp;lt;entropyThreshold&amp;gt;" />
        <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
        <param name="consensus_determination_model" type="select" label="Consensus Determination Model" help="-model,--consensusDeterminationModel &amp;lt;consensusDeterminationModel&amp;gt;">
          <option value="KNOWNS_ONLY">KNOWNS_ONLY</option>
          <option value="USE_READS" selected="True">USE_READS</option>

        <param name="max_insert_size_for_movement" type="integer" value="3000" label="Maximum insert size of read pairs that we attempt to realign" help="-maxIsize,--maxIsizeForMovement &amp;lt;maxIsizeForMovement&amp;gt;" />
        <param name="max_positional_move_allowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,--maxPositionalMoveAllowed &amp;lt;maxPositionalMoveAllowed&amp;gt;" />
        <param name="max_consensuses" type="integer" value="30" label="Max alternate consensuses to try" help="-maxConsensuses,--maxConsensuses &amp;lt;maxConsensuses&amp;gt;" />
        <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" help="-greedy,--maxReadsForConsensuses &amp;lt;maxReadsForConsensuses&amp;gt;" />
        <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,--maxReadsForRealignment &amp;lt;maxReadsForRealignment&amp;gt;" />
        <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,--noOriginalAlignmentTags"/> 
    </expand>
  </inputs>
  <outputs>
    <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />

          <param name="max_positional_move_allowed" value="200" />
          <param name="max_consensuses" value="30" />
          <param name="max_reads_for_consensuses" value="120" />
          <param name="max_reads_for_realignment" value="20000" />
          <param name="no_original_alignment_tags" />
          <output name="output_bam" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" lines_diff="2" /> 
          <output name="output_log" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains" compare="contains" />
      </test>
  </tests>
  <help>
**What it does**

6:35c00763cb5c

<tool id="gatk2_indel_realigner" name="Indel Realigner" version="@VERSION@.1">
  <description>- perform 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":

        -R "${reference_source.ref_file.fields.path}"
    #end if
   -LOD "${lod_threshold}"
    ${knowns_only}
   '

    #set $rod_binding_names = dict()
    #for $rod_binding in $rod_bind:
        #if str( $rod_binding.rod_bind_type.rod_bind_type_selector ) == 'custom':
            #set $rod_bind_name = $rod_binding.rod_bind_type.custom_rod_name
        #else
            #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
    -d "-targetIntervals" "${target_intervals}" "${target_intervals.ext}" "gatk_target_intervals"
    -p '
    --disable_bam_indexing

        ${analysis_param_type.no_original_alignment_tags}
        '
    #end if
  </command>
  <inputs>

    <conditional name="reference_source">
      <expand macro="reference_source_selector_param" />
      <when value="cached">
        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_file&amp;gt;">
          <validator type="unspecified_build" />

          </when>
        </conditional>
    </repeat>
    <param name="lod_threshold" type="float" value="5.0" label="LOD threshold above which the realigner will proceed to realign" help="-LOD,--LODThresholdForCleaning &amp;lt;LODThresholdForCleaning&amp;gt;" />
    <param name="knowns_only" type="boolean" checked="False" truevalue="-knownsOnly" falsevalue="" label="Use only known indels provided as RODs" help="-knownsOnly"/>

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

    <expand macro="analysis_type_conditional">

        <param name="entropy_threshold" type="float" value="0.15" label="percentage of mismatching base quality scores at a position to be considered having high entropy" help="-entropy,--entropyThreshold &amp;lt;entropyThreshold&amp;gt;" />
        <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM" help="-simplifyBAM,--simplifyBAM"/>
        <param name="consensus_determination_model" type="select" label="Consensus Determination Model" help="-model,--consensusDeterminationModel &amp;lt;consensusDeterminationModel&amp;gt;">
          <option value="KNOWNS_ONLY">KNOWNS_ONLY</option>
          <option value="USE_READS" selected="True">USE_READS</option>

        <param name="max_insert_size_for_movement" type="integer" value="3000" label="Maximum insert size of read pairs that we attempt to realign" help="-maxIsize,--maxIsizeForMovement &amp;lt;maxIsizeForMovement&amp;gt;" />
        <param name="max_positional_move_allowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,--maxPositionalMoveAllowed &amp;lt;maxPositionalMoveAllowed&amp;gt;" />
        <param name="max_consensuses" type="integer" value="30" label="Max alternate consensuses to try" help="-maxConsensuses,--maxConsensuses &amp;lt;maxConsensuses&amp;gt;" />
        <param name="max_reads_for_consensuses" type="integer" value="120" label="Max reads (chosen randomly) used for finding the potential alternate consensuses" help="-greedy,--maxReadsForConsensuses &amp;lt;maxReadsForConsensuses&amp;gt;" />
        <param name="max_reads_for_realignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,--maxReadsForRealignment &amp;lt;maxReadsForRealignment&amp;gt;" />
        <param name="no_original_alignment_tags" type="boolean" checked="False" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,--noOriginalAlignmentTags"/>
    </expand>
  </inputs>
  <outputs>
    <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" />
    <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" />

          <param name="max_positional_move_allowed" value="200" />
          <param name="max_consensuses" value="30" />
          <param name="max_reads_for_consensuses" value="120" />
          <param name="max_reads_for_realignment" value="20000" />
          <param name="no_original_alignment_tags" />
          <output name="output_bam" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" lines_diff="2" />
          <output name="output_log" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains" compare="contains" />
      </test>
  </tests>
  <help>
**What it does**