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<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="1.56.0">
  <description>for targeted resequencing data</description>
  <command interpreter="python">

    picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --datatype "$input_file.ext"
    --baitbed "$bait_bed" --targetbed "$target_bed" -n "$out_prefix" --tmpdir "${__new_file_path__}"
    -j "\$JAVA_JAR_PATH/CalculateHsMetrics.jar"

  </command>
  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
  <inputs>
    <param format="sam,bam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" />
    <param name="out_prefix" value="Picard HS Metrics" type="text" label="Title for the output file" help="Use to remind you what the job was for." size="80" />
    <param name="bait_bed" type="data" format="bed,interval" label="Bait intervals: Sequences for bait in the design" help="Note specific format requirements below!" size="80" />
    <param name="target_bed" type="data" format="bed,interval" label="Target intervals: Sequences for targets in the design" help="Note specific format requirements below!" size="80" />
    <!--
    
    Users can be enabled to set Java heap size by uncommenting this option and adding '-x "$maxheap"' to the <command> tag.
    If commented out the heapsize defaults to the value specified within picard_wrapper.py
    
    <param name="maxheap" type="select" 
       help="If in doubt, try the default. If it fails with a complaint about java heap size, try increasing it please - larger jobs will require your own hardware."
     label="Java heap size">
    <option value="4G" selected = "true">4GB default </option>
    <option value="8G" >8GB use if 4GB fails</option>
    <option value="16G">16GB - try this if 8GB fails</option>
    </param>
    
    -->
  </inputs>
  <outputs>
    <data format="html" name="html_file" label="${out_prefix}.html" />
  </outputs>
  <tests>
    <test>
      <!-- Uncomment this if maxheap parameter is enabled
      <param name="maxheap" value="8G"  />
      -->
      <param name="out_prefix" value="HSMetrics" />
      <param name="input_file" value="picard_input_summary_alignment_stats.sam" ftype="sam" />
      <param name="bait_bed" value="picard_input_bait.bed" />
      <param name="target_bed" value="picard_input_bait.bed"  />
      <output name="html_file" file="picard_output_hs_transposed_summary_alignment_stats.html" ftype="html" lines_diff="212"/>
    </test>
  </tests>
  <help>

.. class:: infomark

**Summary**

Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file.

.. class:: warnmark

**WARNING about bait and target files**

Picard is very fussy about the bait and target file format. If these are not exactly right, it will fail with an error something like:

Exception in thread "main" net.sf.picard.PicardException: Invalid interval record contains 6 fields: chr1       45787123        45787316      CASO_22G_25063  1000    +

If you see an error like that from this tool, please do NOT report it to any of the Galaxy mailing lists as it is not a bug! 
It means you must reformat your bait and target files. Galaxy cannot do that for you automatically unfortunately.

The required definition is described in the documentation at http://www.broadinstitute.org/gsa/wiki/index.php/Built-in_command-line_arguments
and the sample provided looks like this:

chr1    1104841 1104940 +       target_1
chr1    1105283 1105599 +       target_2
chr1    1105712 1105860 +       target_3
chr1    1105960 1106119 +       target_4

So your bait and target files MUST have 5 columns with chr, start, end, strand and name tab delimited and in exactly that order.
Note that the Picard mandated sam header described in the documentation linked above is automagically added by the tool in Galaxy.

.. class:: infomark

**Picard documentation**

This is a Galaxy wrapper for CalculateHsMetrics.jar, a part of the external package Picard-tools_.

 .. _Picard-tools: http://www.google.com/search?q=picard+samtools

-----

.. class:: infomark

**Inputs, outputs, and parameters**

Picard documentation says (reformatted for Galaxy):

Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file.

.. csv-table::
   :header-rows: 1

   "Option", "Description"
   "BAIT_INTERVALS=File","An interval list file that contains the locations of the baits used. Required."
   "TARGET_INTERVALS=File","An interval list file that contains the locations of the targets. Required."
   "INPUT=File","An aligned SAM or BAM file. Required."
   "OUTPUT=File","The output file to write the metrics to. Required. Cannot be used in conjuction with option(s) METRICS_FILE (M)"
   "METRICS_FILE=File","Legacy synonym for OUTPUT, should not be used. Required. Cannot be used in conjuction with option(s) OUTPUT (O)"
   "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false"

HsMetrics

 The set of metrics captured that are specific to a hybrid selection analysis.

Output Column Definitions::

  1. BAIT_SET: The name of the bait set used in the hybrid selection.
  2. GENOME_SIZE: The number of bases in the reference genome used for alignment.
  3. BAIT_TERRITORY: The number of bases which have one or more baits on top of them.
  4. TARGET_TERRITORY: The unique number of target bases in the experiment where target is usually exons etc.
  5. BAIT_DESIGN_EFFICIENCY: Target terrirtoy / bait territory. 1 == perfectly efficient, 0.5 = half of baited bases are not target.
  6. TOTAL_READS: The total number of reads in the SAM or BAM file examine.
  7. PF_READS: The number of reads that pass the vendor's filter.
  8. PF_UNIQUE_READS: The number of PF reads that are not marked as duplicates.
  9. PCT_PF_READS: PF reads / total reads. The percent of reads passing filter.
 10. PCT_PF_UQ_READS: PF Unique Reads / Total Reads.
 11. PF_UQ_READS_ALIGNED: The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.
 12. PCT_PF_UQ_READS_ALIGNED: PF Reads Aligned / PF Reads.
 13. PF_UQ_BASES_ALIGNED: The number of bases in the PF aligned reads that are mapped to a reference base. Accounts for clipping and gaps.
 14. ON_BAIT_BASES: The number of PF aligned bases that mapped to a baited region of the genome.
 15. NEAR_BAIT_BASES: The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region.
 16. OFF_BAIT_BASES: The number of PF aligned bases that mapped to neither on or near a bait.
 17. ON_TARGET_BASES: The number of PF aligned bases that mapped to a targetted region of the genome.
 18. PCT_SELECTED_BASES: On+Near Bait Bases / PF Bases Aligned.
 19. PCT_OFF_BAIT: The percentage of aligned PF bases that mapped neither on or near a bait.
 20. ON_BAIT_VS_SELECTED: The percentage of on+near bait bases that are on as opposed to near.
 21. MEAN_BAIT_COVERAGE: The mean coverage of all baits in the experiment.
 22. MEAN_TARGET_COVERAGE: The mean coverage of targets that recieved at least coverage depth = 2 at one base.
 23. PCT_USABLE_BASES_ON_BAIT: The number of aligned, de-duped, on-bait bases out of the PF bases available.
 24. PCT_USABLE_BASES_ON_TARGET: The number of aligned, de-duped, on-target bases out of the PF bases available.
 25. FOLD_ENRICHMENT: The fold by which the baited region has been amplified above genomic background.
 26. ZERO_CVG_TARGETS_PCT: The number of targets that did not reach coverage=2 over any base.
 27. FOLD_80_BASE_PENALTY: The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
 28. PCT_TARGET_BASES_2X: The percentage of ALL target bases acheiving 2X or greater coverage.
 29. PCT_TARGET_BASES_10X: The percentage of ALL target bases acheiving 10X or greater coverage.
 30. PCT_TARGET_BASES_20X: The percentage of ALL target bases acheiving 20X or greater coverage.
 31. PCT_TARGET_BASES_30X: The percentage of ALL target bases acheiving 30X or greater coverage.
 32. HS_LIBRARY_SIZE: The estimated number of unique molecules in the selected part of the library.
 33. HS_PENALTY_10X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 10X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 10 * HS_PENALTY_10X.
 34. HS_PENALTY_20X: The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 20 * HS_PENALTY_20X.
 35. HS_PENALTY_30X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 30 * HS_PENALTY_30X.

.. class:: warningmark

**Warning on SAM/BAM quality**

Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears to be the only way to deal with SAM/BAM that cannot be parsed.


  </help>
</tool>