<tool id="bsmap" name="BSMAP Mapper">
	<requirements>
	    <requirement type='package' version="2.6">bsmap</requirement>
	</requirements>
        <command interpreter="bash">
              bsmap_wrapper.sh
			##Reference genome
			##ref="${reference.fields.path}"
			#if $refGenomeSource.genomeSource == "history":
				ref="${refGenomeSource.myFile}"
			#else
				ref="${refGenomeSource.builtinFile.fields.path}"
			#end if
			##Output files (SAM output, BSMAP summary)
			mapped=$mapped
			##Temp directory
			tempdir=$mapped.files_path
			summary=$summary
			#if str($singlePaired.sPaired) == "single":
			  library="single"
			  mate1=$singlePaired.sInput1
			  #if str($singlePaired.sParams.sSettingsType) == "full":
			    fullparam=true
			    qual=$singlePaired.sParams.qual
			    threshold=$singlePaired.sParams.threshold
			    lowqual=$singlePaired.sParams.lowqual
			    adapter=$singlePaired.sParams.adapter
			    firstn=$singlePaired.sParams.firstn
			    repeat_reads=$singlePaired.sParams.repeat_reads
			    seed_size=$singlePaired.sParams.seed_size
			    mismatch=$singlePaired.sParams.mismatch
			    equal_best=$singlePaired.sParams.equal_best
			    start=$singlePaired.sParams.start
			    end=$singlePaired.sParams.end
			    index_interval=$singlePaired.sParams.index_interval
			    seed_random=$singlePaired.sParams.seed_random
			    rrbs=$singlePaired.sParams.rrbs
			    mode=$singlePaired.sParams.mode
			    align_info=$singlePaired.sParams.align_info     
			  #end if
			#else:
			  library="paired"
			  mate1=$singlePaired.pInput1
			  mate2=$singlePaired.pInput2
			  unpaired=$unpaired
			  #if str($singlePaired.pParams.pSettingsType) == "full":    
			    fullparam=true
			    qual=$singlePaired.pParams.qual
			    threshold=$singlePaired.pParams.threshold
			    lowqual=$singlePaired.pParams.lowqual
			    adapter=$singlePaired.pParams.adapter
			    firstn=$singlePaired.pParams.firstn
			    repeat_reads=$singlePaired.pParams.repeat_reads
			    seed_size=$singlePaired.pParams.seed_size
			    mismatch=$singlePaired.pParams.mismatch
			    equal_best=$singlePaired.pParams.equal_best
			    start=$singlePaired.pParams.start
			    end=$singlePaired.pParams.end
			    index_interval=$singlePaired.pParams.index_interval
			    seed_random=$singlePaired.pParams.seed_random
			    rrbs=$singlePaired.pParams.rrbs
			    mode=$singlePaired.pParams.mode
			    align_info=$singlePaired.pParams.align_info     
			    maxinsert=$singlePaired.pParams.maxinsert  
			    mininsert=$singlePaired.pParams.mininsert  
			  #end if
			#end if
        </command>
  <inputs>

  <conditional name="refGenomeSource">
      <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in reference?">
        <option value="builtin">Use a built-in reference</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="builtin">
        <param name="builtinFile" type="select" label="Select the reference genome">
          <options from_data_table="bsmap_fasta">
            <filter type="sort_by" column="2" />
            <validator type="no_options" message="No reference genomes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="myFile" type="data" format="fasta" label="Select the reference genome" />
      </when> 
  </conditional>
  
  <conditional name="singlePaired">
      <param name="sPaired" type="select" label="Is this library mate-paired?">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
      </param>
      <when value="single">
        <param name="sInput1" type="data" format="fastq,fasta" label="FASTQ file" help="Must have ASCII encoded quality scores"/>
        <conditional name="sParams">
          <param name="sSettingsType" type="select" label="BSMAP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
            <option value="preSet">Commonly used</option>
            <option value="full">Full parameter list</option>
          </param>
          <when value="preSet" />
          <when value="full">
	    <param name="qual" type="select" label="Select the type of FastQ qualities">
		<option value="33">phred33-quals</option>
		<option value="64">phred64-quals</option>
	    </param>
	    <param name="threshold" type="integer" value="0" label="Quality threshold in trimming" help="0-40, default=0 (no trim)" min="0" max="40" />
	    <param name="lowqual" type="integer" value="5" label="Filter low-quality reads containing >n Ns" help="default=5" />
	    <param name="adapter" type="text" value="none" label="3-end adapter sequence" help="default: none (no trim)" />
	    <param name="firstn" type="integer" value="144" label="Map the first N nucleotides of the read" help="default:144 (map the whole read)" />
	    
	    <param name="repeat_reads" type="select" label="How to report repeat hits">
	      <option value="0">none(unique hit only)</option>
	      <option value="1">random one</option>
	    </param>
	    
	    <param name="seed_size" type="integer" value="16" label="Seed size" min="8" max="16" help="default=16(WGBS mode), 12(RRBS mode)" />
	    <param name="mismatch" type="integer" value="2" label="Maximum number of mismatches allowed on a read" max="15" />
	    <param name="equal_best" type="integer" value="20" label="Maximum number of equal best hits to count" max="1000" />
	    <param name="start" type="integer" value="1" label="Start from the Nth read or read pair" />
	    <param name="end" type="integer" value="4294967295" label="End at the Nth read or read pair" />
	    <param name="index_interval" type="integer" value="4" label="Index interval" />
	    <param name="seed_random" type="integer" value="-1" label="Seed for random number generation used in selecting multiple hits" help="other seed values generate pseudo random number based on read index number, to allow reproducible mapping results" />
	    <param name="rrbs" type="text" value="none" label="Activating RRBS mapping mode and set restriction enzyme digestion sites" help="digestion position marked by '-', example: -D C-CGG for MspI digestion. default: none (whole genome shotgun bisulfite mapping mode)" />
	     <param name="mode" type="select" label="Set mapping strand information">
		<option value="0">only map to 2 forward strands</option>
		<option value="1">map SE or PE reads to all 4 strands</option>
	    </param>
	    <param name="align_info" type="text" value="none" label="Set alignment information for the additional nucleotide transition" help="is in the form of two different nucleotides N1N2,indicating N1 in the reads could be mapped to N2 in the reference sequences. default: -M TC, corresponds to C=>U(T) transition in bisulfite conversion. example: -M GA could be used to detect A=>I(G) transition in RNA editing." />
          </when> <!-- full -->
        </conditional> <!-- sParams -->
      </when> <!-- single -->
   
      <when value="paired">
        <param name="pInput1" type="data" format="fastq,fasta" label="Forward FASTQ file" />
	<param name="pInput2" type="data" format="fastq,fasta" label="Reverse FASTQ file" />

        <conditional name="pParams">
          <param name="pSettingsType" type="select" label="BSMAP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list">
            <option value="preSet">Commonly used</option>
            <option value="full">Full parameter list</option>
          </param>
         <when value="preSet" />
          <when value="full">
	    <param name="qual" type="select" label="Select the type of FastQ qualities">
		<option value="33">phred33-quals</option>
		<option value="64">phred64-quals</option>
	    </param>
	    
	    <param name="mininsert" type="integer" value="28" label="Minimal insert size allowed" />
	    <param name="maxinsert" type="integer" value="500" label="Maximal insert size allowed" />
	    
	    <param name="threshold" type="integer" value="0" label="Quality threshold in trimming" help="0-40, default=0 (no trim)" min="0" max="40" />
	    <param name="lowqual" type="integer" value="5" label="Filter low-quality reads containing >n Ns" help="default=5" />
	    <param name="adapter" type="text" value="none" label="3-end adapter sequence" help="default: none (no trim)" />
	    <param name="firstn" type="integer" value="144" label="Map the first N nucleotides of the read" help="default:144 (map the whole read)" />
	    
	    <param name="repeat_reads" type="select" label="How to report repeat hits">
	      <option value="0">none(unique hit only)</option>
	      <option value="1">random one</option>
	    </param>
	    
	    <param name="seed_size" type="integer" value="16" label="Seed size" min="8" max="16" help="default=16(WGBS mode), 12(RRBS mode)" />
	    <param name="mismatch" type="integer" value="2" label="Maximum number of mismatches allowed on a read" max="15" />
	    <param name="equal_best" type="integer" value="20" label="Maximum number of equal best hits to count" max="1000" />
	    <param name="start" type="integer" value="1" label="Start from the Nth read or read pair" />
	    <param name="end" type="integer" value="4294967295" label="End at the Nth read or read pair" />
	    <param name="index_interval" type="integer" value="4" label="Index interval" />
	    <param name="seed_random" type="integer" value="-1" label="Seed for random number generation used in selecting multiple hits" help="other seed values generate pseudo random number based on read index number, to allow reproducible mapping results" />
	    <param name="rrbs" type="text" value="none" label="Activating RRBS mapping mode and set restriction enzyme digestion sites" help="digestion position marked by '-', example: -D C-CGG for MspI digestion. default: none (whole genome shotgun bisulfite mapping mode)" />
	     <param name="mode" type="select" label="Set mapping strand information">
		<option value="0">only map to 2 forward strands</option>
		<option value="1">map SE or PE reads to all 4 strands</option>
	    </param>
	    <param name="align_info" type="text" value="none" label="Set alignment information for the additional nucleotide transition" help="is in the form of two different nucleotides N1N2,indicating N1 in the reads could be mapped to N2 in the reference sequences. default: -M TC, corresponds to C=>U(T) transition in bisulfite conversion. example: -M GA could be used to detect A=>I(G) transition in RNA editing." />

	    
          </when> <!-- full -->
        </conditional> <!-- pParams -->
      </when> <!-- paired -->
    </conditional> <!-- singlePaired -->
  
  
 </inputs>
 <outputs>
        <data name="mapped" format="sam" label="BSMAP Mapped Reads" />
	<data name="summary" format="txt" label="BSMAP Mapping Summary" />
	<data name="unpaired" format ="sam" label="BSMAP Unpaired Hits">
	  <filter>(singlePaired['sPaired'] == 'paired')</filter>
	</data>

 </outputs>
 <help>
**What it does**

BSMAP is a short reads mapping software for bisulfite sequencing reads. It has the following features:

   - read length up to 144 nt, allow up to 15 mismatches, gap size up to 3 bp.

   - support single end and pair end mapping. support multi-thread mapping.

   - support both "Lister protocol" (sequence 2 forward strands only) and "Cokus protocol" (sequence all 4 bisulfite converted strands)

   - reads are directly mapped to original reference genome sequence, no need to preprocess the reads and reference genome to convert C to T.

   - support both whole genome bisulfite sequencing (WGBS) mode and reduced representation bisulfite sequencing (RRBS) mode, allow changing the digestion site information to support different digestion enzymes for RRBS.

   - allow trimming adapter sequences and low quality nucleotides from the 3'end of reads

   - allow trade off between speed/memory usage/mapping sensitivity. For human genome, the RRBS mode uses ~3GB. In WGBS mode, the typical memory usage is ~9GB, but can be as low as 5GB.

   - allow alignment for other nucleotide transitions, for example, can be set to detect the A=>I(G) transition in RNA editing.

.. _BSMAP: http://code.google.com/p/bsmap/

**Input formats**

BSMAP accepts files in FASTA/FASTQ format.

**Outputs**

The output contains the following files:

    -  mapped reads in SAM format
    
    -  mapping summary
    
    -  unpaired hits (only for paired-end mapping)
   
 </help>
 
 <tests>
 </tests>
</tool>