<tool id="gatk_table_recalibration" name="Table Recalibration" version="0.0.1">
  <description>on BAM files</description>
  <command interpreter="python">gatk_wrapper.py
   --stdout "${output_log}"
   -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
   -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
   -p 'java 
    -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar"
    -T "TableRecalibration"
    -o "${output_bam}"
    -et "NO_ET" ##ET no phone home
    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"
    #end if
    --recal_file "${input_recal}"
    --disable_bam_indexing
   '
    ##start standard gatk options
    #if $gatk_param_type.gatk_param_type_selector == "advanced":
        #for $sample_metadata in $gatk_param_type.sample_metadata:
            -p '--sample_metadata "${sample_metadata.sample_metadata_file}"'
        #end for
        #for $read_filter in $gatk_param_type.read_filter:
            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
            ###raise Exception( str( dir( $read_filter ) ) )
            #for $name, $param in $read_filter.read_filter_type.iteritems():
                #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                    --${name} "${param}"
                #end if
            #end for
            '
        #end for
        #if str( $gatk_param_type.input_intervals ) != "None":
            -d "-L" "${gatk_param_type.input_intervals}" "${gatk_param_type.input_intervals.ext}" "input_intervals"
        #end if
        #if str( $gatk_param_type.input_exclude_intervals ) != "None":
            -d "-XL" "${gatk_param_type.input_exclude_intervals}" "${gatk_param_type.input_exclude_intervals.ext}" "input_intervals"
        #end if
        #set $rod_binding_names = dict()
        #for $rod_binding in $gatk_param_type.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( $rod_bind_name, -1 ) + 1
            -d "-B:${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]}"
            #if str( $rod_binding.rod_bind_type.rodToIntervalTrackName ):
                -p '--rodToIntervalTrackName "${rod_bind_name}"'
            #end if
        #end for
        -p '--BTI_merge_rule "${gatk_param_type.BTI_merge_rule}"'
        #if str( $gatk_param_type.input_dbsnp_rod ) != "None":
            -d "-D" "${gatk_param_type.input_dbsnp_rod}" "${gatk_param_type.input_dbsnp_rod.ext}" "dbsnp_rod"
        #end if
        -p '--downsampling_type "${gatk_param_type.downsampling_type.downsampling_type_selector}"'
        #if str( $gatk_param_type.downsampling_type.downsampling_type_selector ) != "NONE":
            -p '--${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_type_selector} "${gatk_param_type.downsampling_type.downsample_to_type.downsample_to_value}"'
        #end if
        -p '
        --baq "${gatk_param_type.baq}"
        --baqGapOpenPenalty "${gatk_param_type.baq_gap_open_penalty}"
        ${gatk_param_type.use_original_qualities}
        --defaultBaseQualities "${gatk_param_type.default_base_qualities}"
        --validation_strictness "${gatk_param_type.validation_strictness}"
        --interval_merging "${gatk_param_type.interval_merging}"
        '
        #if str( $gatk_param_type.read_group_black_list ) != "None":
            -d "-read_group_black_list" "${gatk_param_type.read_group_black_list}" "txt" "input_read_group_black_list"
        #end if
    #end if
    #if str( $reference_source.reference_source_selector ) == "history":
        -d "-R" "${reference_source.ref_file}" "${reference_source.ref_file.ext}" "gatk_input"
    #end if
    ##end standard gatk options
    
    ##start analysis specific options
    #if $analysis_param_type.analysis_param_type_selector == "advanced":
        -p '
        #if $analysis_param_type.default_read_group_type.default_read_group_type_selector == "set":
            --default_read_group "${analysis_param_type.default_read_group_type.default_read_group}"
        #end if
        #if str( $analysis_param_type.default_platform ) != "default":
            --default_platform "${analysis_param_type.default_platform}"
        #end if
        #if str( $analysis_param_type.force_read_group_type.force_read_group_type_selector ) == "set":
            --force_read_group "${analysis_param_type.force_read_group_type.force_read_group}"
        #end if
        #if str( $analysis_param_type.force_platform ) != "default":
            --force_platform "${analysis_param_type.force_platform}"
        #end if
        ${analysis_param_type.exception_if_no_tile}
        #if str( $analysis_param_type.solid_options_type.solid_options_type_selector ) == "set":
            #if str( $analysis_param_type.solid_options_type.solid_recal_mode ) != "default":
                --solid_recal_mode "${analysis_param_type.solid_options_type.solid_recal_mode}" 
            #end if
            #if str( $analysis_param_type.solid_options_type.solid_nocall_strategy ) != "default":
                --solid_nocall_strategy "${analysis_param_type.solid_options_type.solid_nocall_strategy}" 
            #end if
        #end if
        ${analysis_param_type.simplify_bam}
        --preserve_qscores_less_than "${analysis_param_type.preserve_qscores_less_than}"
        --smoothing "${analysis_param_type.smoothing}"
        --max_quality_score "${analysis_param_type.max_quality_score}"
        --window_size_nqs "${analysis_param_type.window_size_nqs}"
        --homopolymer_nback "${analysis_param_type.homopolymer_nback}"
        ${analysis_param_type.do_not_write_original_quals}
        '
    #end if
  </command>
  <inputs>
    <param name="input_recal" type="data" format="csv" label="Covariates table recalibration file" />
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
        <option value="cached">Locally cached</option>
        <option value="history">History</option>
      </param>
      <when value="cached">
        <param name="input_bam" type="data" format="bam" label="BAM file">
          <validator type="unspecified_build" />
          <validator type="dataset_metadata_in_file" filename="picard_index.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
        </param>
        <param name="ref_file" type="select" label="Using reference genome">
          <options from_data_table="picard_indexes">
            <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
          </options>
        </param>
      </when>
      <when value="history"> <!-- FIX ME!!!! -->
        <param name="input_bam" type="data" format="bam" label="BAM file" />
        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
      </when>
    </conditional>
    
    <conditional name="gatk_param_type">
      <param name="gatk_param_type_selector" type="select" label="Basic or Advanced GATK options">
        <option value="basic" selected="True">Basic</option>
        <option value="advanced">Advanced</option>
      </param>
      <when value="basic">
        <!-- Do nothing here -->
      </when>
      <when value="advanced">
        <repeat name="sample_metadata" title="Sample Metadata">
            <param name="sample_metadata_file" type="data" format="txt" label="Sample file(s) in JSON format" />
        </repeat>
        <repeat name="read_filter" title="Read Filter">
            <conditional name="read_filter_type">
		      <param name="read_filter_type_selector" type="select" label="Read Filter Type">
		        <option value="MaxReadLength" selected="True">MaxReadLength</option>
		        <option value="ZeroMappingQualityRead">ZeroMappingQualityRead</option>
		      </param>
	          <when value="ZeroMappingQualityRead">
	              <!-- no extra options -->
	          </when>
	          <when value="MaxReadLength">
	              <param name="maxReadLength" type="integer" value="76" label="Max Read Length"/>
	          </when>
            </conditional>
        </repeat>
        <param name="input_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals over which to operate" />
        <param name="input_exclude_intervals" type="data" format="picard_interval_list" optional="True" label="A list of genomic intervals to exclude from processing" />
        <repeat name="rod_bind" title="Binding for reference-ordered data">
            <conditional name="rod_bind_type">
		      <param name="rod_bind_type_selector" type="select" label="Binding Type">
		        <option value="snps" selected="True">SNPs</option>
		        <option value="indels">INDELs</option>
		        <option value="custom">Custom</option>
		      </param>
	          <when value="snps">
	              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
	              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
	          </when>
	          <when value="indels">
	              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
	              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
	          </when>
	          <when value="custom">
	              <param name="custom_rod_name" type="text" value="Unknown" label="ROD Name"/>
	              <param name="input_rod" type="data" format="vcf,gatk_dbsnp,bed" label="ROD file" />
	              <param name="rodToIntervalTrackName" type="boolean" truevalue="--rodToIntervalTrackName" falsevalue="" label="Use ROD as interval List (-BTI, --rodToIntervalTrackName)" help="Only one ROD may have this option specified" />
	          </when>
            </conditional>
        </repeat>
        <param name="BTI_merge_rule" type="select" label="BTI merge rule">
          <option value="UNION" selected="True">UNION</option>
          <option value="INTERSECTION">INTERSECTION</option>
        </param>
        <param name="input_dbsnp_rod" type="data" format="gatk_dbsnp" optional="True" label="dbSNP reference ordered data (ROD)" />
        <conditional name="downsampling_type">
          <param name="downsampling_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
            <option value="NONE" selected="True">NONE</option>
            <option value="ALL_READS">ALL_READS</option>
            <option value="BY_SAMPLE">BY_SAMPLE</option>
          </param>
          <when value="NONE">
	          <!-- no more options here -->
	      </when>
          <when value="ALL_READS">
	          <conditional name="downsample_to_type">
	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
	              </param>
	              <when value="downsample_to_fraction">
	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
	              </when>
	              <when value="downsample_to_coverage">
	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
	              </when>
	          </conditional>
	      </when>
          <when value="BY_SAMPLE">
	          <conditional name="downsample_to_type">
	              <param name="downsample_to_type_selector" type="select" label="Type of reads downsampling to employ at a given locus" help="Downsampling Type">
	                  <option value="downsample_to_fraction" selected="True">Downsample by Fraction</option>
	                  <option value="downsample_to_coverage">Downsample by Coverage</option>
	              </param>
	              <when value="downsample_to_fraction">
	                  <param name="downsample_to_value" type="float" label="Fraction [0.0-1.0] of reads to downsample to" value="0.1"/>
	              </when>
	              <when value="downsample_to_coverage">
	                  <param name="downsample_to_value" type="integer" label="Coverage to downsample to at any given locus" value="0"/>
	              </when>
	          </conditional>
	      </when>
        </conditional>
        <param name="baq" type="select" label="Type of BAQ calculation to apply in the engine">
          <option value="OFF" selected="True">OFF</option>
          <option value="CALCULATE_AS_NECESSARY">CALCULATE_AS_NECESSARY</option>
          <option value="RECALCULATE">RECALCULATE</option>
        </param>
        <param name="baq_gap_open_penalty" type="integer" label="BAQ gap open penalty (Phred Scaled)" value="40" help="Default value is 40. 30 is perhaps better for whole genome call sets."/>
        <param name="use_original_qualities" type="boolean" truevalue="--useOriginalQualities" falsevalue="" label="Use the original base quality scores from the OQ tag" />
        <param name="default_base_qualities" type="integer" label="Value to be used for all base quality scores, when some are missing" value="-1"/>
        <param name="validation_strictness" type="select" label="How strict should we be with validation">
          <option value="STRICT" selected="True">STRICT</option>
          <option value="LENIENT">LENIENT</option>
          <option value="SILENT">SILENT</option>
        </param>
        <param name="interval_merging" type="select" label="Interval merging rule">
          <option value="ALL" selected="True">ALL</option>
          <option value="OVERLAPPING_ONLY">OVERLAPPING_ONLY</option>
        </param>
        <param name="read_group_black_list" type="data" format="txt" optional="True" label="Read group black list" />
      </when>
    </conditional>
    
    
    <conditional name="analysis_param_type">
      <param name="analysis_param_type_selector" type="select" label="Basic or Advanced Analysis options">
        <option value="basic" selected="True">Basic</option>
        <option value="advanced">Advanced</option>
      </param>
      <when value="basic">
        <!-- Do nothing here -->
      </when>
      <when value="advanced">
        <conditional name="default_read_group_type">
          <param name="default_read_group_type_selector" type="select" label="Set default Read Group">
            <option value="default" selected="True">Don't Set</option>
            <option value="set">Set</option>
          </param>
          <when value="default">
            <!-- do nothing here -->
          </when>
          <when value="set">
            <param name="default_read_group" type="text" value="Unknown" label="If a read has no read group then default to the provided String"/>
          </when>
        </conditional>
        <param name="default_platform" type="select" label="Set default Platform">
          <option value="default" selected="True">Don't Set</option>
          <option value="illumina">illumina</option>
          <option value="454">454</option>
          <option value="solid">solid</option>
        </param>
        <conditional name="force_read_group_type">
          <param name="force_read_group_type_selector" type="select" label="Force Read Group">
            <option value="default" selected="True">Don't Force</option>
            <option value="set">Force</option>
          </param>
          <when value="default">
            <!-- do nothing here -->
          </when>
          <when value="set">
            <param name="force_read_group" type="text" value="Unknown" label="If provided, the read group ID of EVERY read will be forced to be the provided String."/>
          </when>
        </conditional>
        <param name="force_platform" type="select" label="Force Platform">
          <option value="default" selected="True">Don't Force</option>
          <option value="illumina">illumina</option>
          <option value="454">454</option>
          <option value="solid">solid</option>
        </param>
        <param name="exception_if_no_tile" type="boolean" checked="False" truevalue="--exception_if_no_tile" falsevalue="" label="Throw an exception when no tile can be found"/>
        <conditional name="solid_options_type">
          <param name="solid_options_type_selector" type="select" label="Set SOLiD specific options">
            <option value="default" selected="True">Don't Set</option>
            <option value="set">Set</option>
          </param>
          <when value="default">
            <!-- do nothing here -->
          </when>
          <when value="set">
            <param name="solid_recal_mode" type="select" label="How should we recalibrate solid bases in which the reference was inserted">
              <option value="default" selected="True">Don't set</option>
              <option value="DO_NOTHING">DO_NOTHING</option>
              <option value="SET_Q_ZERO">SET_Q_ZERO</option>
              <option value="SET_Q_ZERO_BASE_N">SET_Q_ZERO_BASE_N</option>
              <option value="REMOVE_REF_BIAS">REMOVE_REF_BIAS</option>
            </param>
            <param name="solid_nocall_strategy" type="select" label="Behavior of the recalibrator when it encounters no calls">
              <option value="default" selected="True">Don't set</option>
              <option value="THROW_EXCEPTION">THROW_EXCEPTION</option>
              <option value="LEAVE_READ_UNRECALIBRATED">LEAVE_READ_UNRECALIBRATED</option>
              <option value="PURGE_READ">PURGE_READ</option>
            </param>
          </when>
        </conditional>
        <param name="simplify_bam" type="boolean" checked="False" truevalue="-simplifyBAM" falsevalue="" label="Simplify BAM"/>
        <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate"/>
        <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" />
        <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated"/>
        <param name="smoothing" type="integer" value="1" label="smoothing"/>
        <param name="max_quality_score" type="integer" value="50" label="Max quality score"/>
        <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag"/>
      </when>
    </conditional>
  </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)" />
  </outputs>
  <tests>
      <test>
          <param name="input_recal" value="gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv" ftype="csv" /> 
          <param name="reference_source_selector" value="history" />
          <param name="ref_file" value="phiX.fasta" ftype="fasta" />
          <param name="input_bam" value="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" />
          <param name="gatk_param_type_selector" value="basic" />
          <param name="analysis_param_type_selector" value="basic" />
          <output name="output_bam" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam" ftype="bam" lines_diff="2" />
          <output name="output_log" file="gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains" compare="contains" />
      </test>
  </tests>
  <help>
**What it does**

     This walker is designed to work as the second pass in a two-pass processing step, doing a by-read traversal.  For 
     each base in each read this walker calculates various user-specified covariates (such as read group, reported 
     quality score, cycle, and dinuc) Using these values as a key in a large hashmap the walker calculates an empirical 
     base quality score and overwrites the quality score currently in the read. This walker then outputs a new bam file 
     with these updated (recalibrated) reads.  Note: This walker expects as input the recalibration table file generated 
     previously by CovariateCounterWalker. Note: This walker is designed to be used in conjunction with 
     CovariateCounterWalker.

------

Please cite the website "http://addlink.here" as well as:

Add citation here 2011.

------

**Input formats**

GenomeAnalysisTK: TableRecalibration accepts an aligned BAM and a recalibration CSV input files.

------

**Outputs**

The output is in BAM format, see http://addlink.here for more details.

-------

**Settings**::

 default_read_group                           If a read has no read group then default to the provided String.
 default_platform                                If a read has no platform then default to the provided String. Valid options are illumina, 454, and solid.
 force_read_group                               If provided, the read group ID of EVERY read will be forced to be the provided String. This is useful to collapse all data into a single read group.
 force_platform                                    If provided, the platform of EVERY read will be forced to be the provided String. Valid options are illumina, 454, and solid.
 window_size_nqs                                 The window size used by MinimumNQSCovariate for its calculation
 homopolymer_nback                           The number of previous bases to look at in HomopolymerCovariate
 exception_if_no_tile                               If provided, TileCovariate will throw an exception when no tile can be found. The default behavior is to use tile = -1
 solid_recal_mode                             How should we recalibrate solid bases in whichthe reference was inserted? Options = DO_NOTHING, SET_Q_ZERO, SET_Q_ZERO_BASE_N, or REMOVE_REF_BIAS (DO_NOTHING|SET_Q_ZERO|SET_Q_ZERO_BASE_N|REMOVE_REF_BIAS)
 solid_nocall_strategy   Defines the behavior of the recalibrator when it encounters no calls in the color space. Options = THROW_EXCEPTION, LEAVE_READ_UNRECALIBRATED, or PURGE_READ (THROW_EXCEPTION|LEAVE_READ_UNRECALIBRATED|PURGE_READ)
 recal_file                                     Filename for the input covariates table recalibration .csv file
 out                                                           The output BAM file
 bam_compression                            Compression level to use for writing BAM files
 disable_bam_indexing                                                   Turn off on-the-fly creation of indices for output BAM files.
 simplifyBAM                                               If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier
 preserve_qscores_less_than            Bases with quality scores less than this threshold won't be recalibrated, default=5. In general it's unsafe to change qualities scores below &lt; 5, since base callers use these values to indicate random or bad bases
 smoothing                                              Number of imaginary counts to add to each bin bin order to smooth out bins with few data points, default=1
 max_quality_score                            The integer value at which to cap the quality scores, default=50
 doNotWriteOriginalQuals                                         If true, we will not write the original quality (OQ) tag for each read

  </help>
</tool>