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<tool id="somatic_sniper_tool" name="Somatic Sniper" version="1.0.2">
  <description>: identify single nucleotide positions that are different between tumor and normal</description>
  <requirements>
        <requirement type="package" version="unstable">somatic-sniper</requirement>	
  </requirements>
  <command interpreter="perl">
  	somatic_sniper_wrapper.pl

  	"NORMAL::$normal"
  	"TUMOR::$tumor"
	"OUTPUT::$snp_output"
  	"OPTION::-F $output"
  	
  	 #if $option.option == "modify_parameters":
  	 	"OPTION::-q $option.readFilter"
  	 	"OPTION::-Q $option.somaticFilter"
  	 	"OPTION::-s $option.mutationPrior"
  	 	#if str($option.disablePriors) == "true" 
  	 		"OPTION::-p"  	 	  	 	
 		#end if
  	 #end if
  	
  	"OPTION::-f $reference.fields.path"  	
	

  </command>
	<inputs>
	<param name="reference" type="select" label="Select a reference genome">
		<options from_data_table="all_fasta">
			<filter type="sort_by" column="2" />
			<validator type="no_options" message="No indexes are available" />
		</options>
	</param>

	<param format="bam" name="normal" type="data" label="Normal sample" help=""/>
	<param format="bam" name="tumor" type="data" label="Tumor Sample" help=""/>
	<param name="output" type="select" label="Output Type" help="" optional="true">
		<option value="classic" selected="true">Classic</option>
		<option value="vcf">VCF</option>
		<option value="bed">BED</option>
	</param>


	<conditional name="option">
		<param name="option" type="select" label="Optional Parameters" help="" optional="true">
			<option value="default_parameters" selected="true">Default Parameters</option>
			<option value="modify_parameters">Modify Parameters</option>
		</param>
		<when value="modify_parameters">
	
			<param name="readFilter" label="filtering reads with mapping quality less than"  type="integer" value="0" optional="true" />
			<param name="somaticFilter" label="filtering somatic snv output with somatic quality less than"  type="integer" value="15" optional="true" />
			<param name="disablePriors" type="select" label="disable priors in the somatic calculation. Increases sensitivity for solid tumors" help="" optional="true">
				<option value="true"  >true</option>
				<option value="false" selected="true">false</option>
			</param>
			<param name="mutationPrior"  label="prior probability of a somatic mutation" type="float" value="0.10000" optional="true" />
      
		</when>
		
	</conditional>

	</inputs>
	<outputs>
		<data name="snp_output" format="text" label="${tool.name} result on ${on_string}" />
	</outputs>
	<help>
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**Reference**
	
  http://gmt.genome.wustl.edu/somatic-sniper/current/
  
-----

**What it does**

The purpose of this program is to identify single nucleotide positions that are different between tumor and normal 
(or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the 
differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood 
model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are 
different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255) 
that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and 
255 means there is a probability of 1 – 10(255/-10) that the genotypes are different between tumor and normal. This is consistent 
with how the SAM format reports such probabilities. 

bam-somaticsniper [options] -f ref.fasta tumor.bam normal.bam snp_output_file

Bam files must contain LB tag in @RG line.
Picard tools can be used to add lines to BAM headers.

-----
 
**Required Parameters**

::

  -f 	FILE REQUIRED reference sequence in the FASTA format

-----

**Options**

::

 -q 	INT    filtering reads with mapping quality less than INT [0]
 
 -Q	INT    filtering somatic snv output with somatic quality less than  INT [15]
        
 -p 	FLAG   disable priors in the somatic calculation. Increases sensitivity for solid tumors
        
 -J 	FLAG   Use prior probabilities accounting for the somatic mutation rate
 
 -s 	FLOAT  prior probability of a somatic mutation (implies -J) [0.010000]
        
 -T 	FLOAT  theta in maq consensus calling model (for -c/-g) [0.850000]
        
 -N 	INT    number of haplotypes in the sample (for -c/-g) [2]
        
 -r 	FLOAT  prior of a difference between two haplotypes (for -c/-g) [0.001000]
        
 -F 	STRING select output format [classic]
        Available formats:
        	classic
        	vcf
        	bed
             
-----            

**File Formats**      
             
::

  Classic:

  Each line contains the following tab-separated values:

    1. Chromosome
    2. Position
    3. Reference base
    4. IUB genotype of tumor
    5. IUB genotype of normal
    6. Somatic Score
    7. Tumor Consensus quality
    8. Tumor variant allele quality
    9. Tumor mean mapping quality
    10. Normal Consensus quality
    11. Normal variant allele quality
    12. Normal mean mapping quality
    13. Depth in tumor (# of reads crossing the position)
    14. Depth in normal (# of reads crossing the position)
    15. Mean base quality of reads supporting reference in tumor
    16. Mean mapping quality of reads supporting reference in tumor
    17. Depth of reads supporting reference in tumor
    18. Mean base quality of reads supporting variant(s) in tumor
    19. Mean mapping quality of reads supporting variant(s) in tumor
    20. Depth of reads supporting variant(s) in tumor
    21. Mean base quality of reads supporting reference in normal
    22. Mean mapping quality of reads supporting reference in normal
    23. Depth of reads supporting reference in normal
    24. Mean base quality of reads supporting variant(s) in normal
    25. Mean mapping quality of reads supporting variant(s) in normal
    26. Depth of reads supporting variant(s) in normal



	</help>
</tool>