<tool id="gatk2_print_reads" name="Print Reads" version="0.0.7">
  <description>on BAM files</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( $reference_source.input_bam.metadata.bam_index ) != "None":
        -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
    #end if
    -p '
    @JAR_PATH@
    -T "PrintReads"
    -o "${output_bam}"
    \$GATK2_SITE_OPTIONS

    ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
    --num_cpu_threads_per_data_thread \${GALAXY_SLOTS:-6}


    #if $reference_source.reference_source_selector != "history":
        -R "${reference_source.ref_file.fields.path}"
    #end if
    #if str($input_recal) != 'None':
        --BQSR "${input_recal}"
    #end if
    --disable_bam_indexing
   '
   
    #include source=$standard_gatk_options#
    
    #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="gatk_report" optional="true" label="Covariates table recalibration file" 
        help="The input covariates table file which enables on-the-fly base quality score recalibration (intended for use with BaseRecalibrator files) (-BQSR,--BQSR)" />
    <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" />
          <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" 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" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" >
          <options from_data_table="gatk2_picard_indexes">
            <filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/>
          </options>
          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
        </param>
      </when>
      <when value="history">
        <param name="input_bam" type="data" format="bam" label="BAM file" help="-I,--input_file &amp;lt;input_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;">
          <options>
            <filter type="data_meta" key="dbkey" ref="input_bam" />
          </options>
        </param>
      </when>
    </conditional>
    
    <expand macro="gatk_param_type_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" help="--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" help="--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" help="--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" help="--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" help="--exception_if_no_tile"/>
        <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" help="-sMode,--solid_recal_mode &amp;lt;solid_recal_mode&amp;gt;">
              <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" help="-solid_nocall_strategy,--solid_nocall_strategy &amp;lt;solid_nocall_strategy&amp;gt;">
              <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" help="-simplifyBAM,--simplifyBAM"/>
        <param name="window_size_nqs" type="integer" value="5" label="Window size used by MinimumNQSCovariate" help="--window_size_nqs"/>
        <param name="homopolymer_nback" type="integer" value="7" label="Number of previous bases to look at in HomopolymerCovariate" help="-nback,--homopolymer_nback &amp;lt;homopolymer_nback&amp;gt;" />
        <param name="preserve_qscores_less_than" type="integer" value="5" label="Bases with quality scores less than this threshold won't be recalibrated" help="-pQ,--preserve_qscores_less_than &amp;lt;preserve_qscores_less_than&amp;gt;"/>
        <param name="smoothing" type="integer" value="1" label="smoothing" help="-sm,--smoothing &amp;lt;smoothing&amp;gt;"/>
        <param name="max_quality_score" type="integer" value="50" label="Max quality score" help="-maxQ,--max_quality_score &amp;lt;max_quality_score&amp;gt;"/>
        <param name="do_not_write_original_quals" type="boolean" checked="False" truevalue="--doNotWriteOriginalQuals" falsevalue="" label="Do Not Write Original Quality tag" help="-noOQs,--doNotWriteOriginalQuals"/>
      </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="4" />
          <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.

For more information on base quality score recalibration using the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_PrintReads.html&gt;`_.

To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.

If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.

------

**Inputs**

GenomeAnalysisTK: PrintReads accepts an aligned BAM and a recalibration (gatk_report) input files.


**Outputs**

The output is in BAM format.


Go `here &lt;http://www.broadinstitute.org/gatk/guide/topic?name=intro&gt;`_ for details on GATK file formats.

-------

**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 .gatk_report 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

@CITATION_SECTION@
  </help>
</tool>