<tool name="Insertion size metrics" id="PicardInsertSize" version="1.56.0">
  <description>for PAIRED data</description>
  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
  <command interpreter="python">
   picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --deviations "$deviations"
   --histwidth "$histWidth" --minpct "$minPct" --malevel "$malevel"
   -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file"
  </command>
  <inputs>
    <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for"
      help="If empty, upload or import a SAM/BAM dataset."/>
    <param name="out_prefix" value="Insertion size metrics" type="text"
      label="Title for the output file" help="Use this remind you what the job was for" size="120" />
    <param name="deviations" value="10.0" type="float"
      label="Deviations" size="5" 
      help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" />
     <param name="histWidth" value="0" type="integer"
      label="Histogram width" size="5" 
      help="Explicitly sets the histogram width option - leave 0 to ignore" />
     <param name="minPct" value="0.05" type="float"
      label="Minimum percentage" size="5" 
      help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" />
     <param name="malevel" value="0" type="select" multiple="true"  label="Metric Accumulation Level"
      help="Level(s) at which metrics will be accumulated">
      <option value="ALL_READS" selected="true">All reads (default)</option>
      <option value="SAMPLE" default="true">Sample</option>
      <option value="LIBRARY" default="true">Library</option>
      <option value="READ_GROUP" default="true">Read group</option>
     </param>
  </inputs>
  <outputs>
    <data format="html" name="html_file" label="InsertSize_${out_prefix}.html"/>
  </outputs>
  <tests>
    <test>
      <param name="input_file" value="picard_input_tiny.sam" />
      <param name="out_prefix" value="Insertion size metrics" />
      <param name="deviations" value="10.0" />
      <param name="histWidth" value="0" />
      <param name="minPct" value="0.01" />
      <param name="malevel" value="ALL_READS" />
      <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" compare="contains" lines_diff="40" />
    </test>
  </tests>
  <help>


.. class:: infomark

**Purpose**

Reads a SAM or BAM file and describes the distribution 
of insert size (excluding duplicates) with metrics and a histogram plot.

**Picard documentation**

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

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

.. class:: warningmark

**Useful for paired data only**

This tool works for paired data only and can be expected to fail for single end data.

-----

.. class:: infomark

**Inputs, outputs, and parameters**

Picard documentation says (reformatted for Galaxy):

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

    Option,Description
    "INPUT=File","SAM or BAM file Required."
    "OUTPUT=File","File to write insert size metrics to Required."
    "HISTOGRAM_FILE=File","File to write insert size histogram chart to Required."
    "TAIL_LIMIT=Integer","When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items. This also limits how much data goes into each data category of the histogram."
    "HISTOGRAM_WIDTH=Integer","Explicitly sets the histogram width, overriding the TAIL_LIMIT option. Also, when calculating mean and stdev, only bins LE HISTOGRAM_WIDTH will be included. "
    "MINIMUM_PCT=Float","When generating the histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads. (Range: 0 to 1) Default value: 0.01."
    "STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0."
    "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false."

.. 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>