<!--
purpose: xml file for BAMEdit tool
author: Ziru Zhou
date: October, 2012
-->
<tool id="BAM_Editor" name="BAMEdit" version="1.1.0">
  <requirements>
    <requirement type="set_environment">SCRIPT_PATH</requirement>
    <requirement type="package" version="0.1.12">samtools</requirement>
    <requirement type="package" version="0.1.12">maq2sam-long</requirement>
  </requirements>
  <description>Merging, splitting, filtering, and QC of BAM files</description>
  <command interpreter="python">bamedit.py $options_file \$SCRIPT_PATH</command>
  <inputs>
    <conditional name="input_type">
      <param name="input_type_selector" type="select" label="Select your BAM command">
  <option value="merge">Merge BAM files</option>
  <option value="split">Split BAM file</option>
  <option value="filter">Filter BAM file</option>
  <option value="pileup">Calculate coverage QC</option>
      </param>

      <when value="merge">
        <param format="bam" name="input1" type="data" label="Select your first input BAM file"/>
  <param format="bam" name="input2" type="data" label="Select your second input BAM file"/>
  <param format="bam" name="input3" type="data" optional="True" label="Select your third input BAM file (optional)" help="Optional third BAM file to be merged."/>
      </when>

      <when value="split">
        <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
      </when>  

      <when value="filter">
        <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
        <param name="quality" type="integer" min="1" value="1" label="Minimum Mapping Quality (MMQ)" help="Quality filter should be 1 or higher."/>
      </when>

      <when value="pileup">
        <param format="bam" name="input1" type="data" label="Select your input BAM file"/>
  <param format="fasta" name="input2" type="data" label="Select your fasta reference file"/>   
  <!--<param name="outopt" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Alternatative output format" help="format: BAM_FILE, REFERENCE_FILE, GENOME_COVERAGE_PERCENTAGE, AVERAGE_COVERAGE_OF_BASES_COVERED"/>-->
      </when>
    </conditional>
 
    <!--<param name="output_name" type="text" value="output" size="30" label="Output file name"/>-->
  </inputs>

  <outputs>
    <data format="bam" name="bamoutm" label="${tool.name}: merge on ${on_string}">
  <filter>input_type['input_type_selector'] == 'merge'</filter>
    </data>
    <data format="bam" name="bamoutf" label="${tool.name}: filter on ${on_string}">
  <filter> input_type['input_type_selector'] == 'filter'</filter>
    </data>
    <data format="bam" name="bamouts1" label="${tool.name}: split on ${on_string} (part 1)">
  <filter>input_type['input_type_selector'] == 'split'</filter>
    </data>
    <data format="bam" name="bamouts2" label="${tool.name}: split on ${on_string} (part2)">
  <filter>input_type['input_type_selector'] == 'split'</filter>
    </data>
    <data format="txt" name="bamoutp" label="${tool.name}: pileup on ${on_string}">
  <filter>input_type['input_type_selector'] == 'pileup'</filter>
    </data>
  </outputs>
  
  <configfiles>
    <configfile name="options_file">&lt;%
import simplejson
%&gt;
#if str($input_type.input_type_selector) == 'merge':
#if str($input_type.input3) != 'None':
#set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2), 'input3':str($input3) }
#else:
#set $__options = { 'action':str("merge"), 'bamout':str($bamoutm), 'input1':str($input1), 'input2':str($input2) }
#end if
#end if
#if str($input_type.input_type_selector) == 'split':
#set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1) }
#end if
#if str($input_type.input_type_selector) == 'filter':
#set $__options = { 'action':str("filter"), 'bamout':str($bamoutf), 'input1':str($input1), 'quality':int($input_type.quality) }
#end if
#if str($input_type.input_type_selector) == 'pileup':
#set $__options = { 'action':str("pileup"), 'bamout':str($bamoutp), 'input1':str($input1), 'input2':str($input2), 'bamname':str($input1.name), 'refname':str($input2.name) }
#end if
${ simplejson.dumps( __options )}
    </configfile>
  </configfiles>
  <tests>
    <test>
  <!--none -->
    </test>
  </tests>

  <help>
**What it does**

Simple interface to manipulate BAM files through the use of SAMtools.

View the original SAMtools documentation: http://samtools.sourceforge.net/

------

**Usage**

**Merge BAM files**: Merges 2 or 3 input BAM files into a single BAM file.

**Split BAM file**: Randomly split input BAM file into 2 BAM files. 

**Filter BAM file**: Removes aligned reads from input BAM files with mapping quality lower than entered Minimum Mapping Quality (MMQ) value.  

**Calculate coverage QC**: Calculates QC metrics such as percentage of genome covered and average coverage of bases covered for the input BAM and reference files.


------

**Citation**

Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]

Written by Ziru Zhou ( ziruzhou@gmail.com ).  Please send your comments/questions to modENCODE DCC at help@modencode.org.

 </help>
</tool>