<?xml version="1.0"?>
<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1">
  <description/>
  <requirements><requirement type="package">mosaik</requirement></requirements>
  <command>
    #set $processors = '-p 4'
    #set $lm = ''
    #if $paired.kind == 'single':
        #set $mfl = ''
        #set $ls  = ''
    #else:
        #set $ls = '-ls $mfl'
    #end if
    MosaikBuild -fr
    #if $genomeSource.refGenomeSource == 'indexed':
        ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] }
    #else:
        $genomeSource.historyReference
    #end if
        -oa mosaik_ref_file;
    MosaikBuild  -q $reads $mfl -st $st -out mosaik_reads_file;
    MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls -mm $mm -mhp $mhp -act $act -bw $bw $processors $lm -hs 15;
    MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file;
    #if str($outFormat) == 'bam':
        samtools sort sam_bam_file sorted_bam;
        mv sorted_bam.bam $output
    #else:
        gunzip sam_bam_file.gz;
        mv sam_bam_file $output
    #end if
  </command>
  <inputs>
    <conditional name="genomeSource">
      <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="indexReference" type="select" label="Select a reference genome">
          <options from_data_table="mosaik_indexes">
            <filter type="sort_by" column="2"/>
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history"/>
      </when>
    </conditional>
    <param format="fastq" name="reads" type="data" label="Fastq Reads File"/>
    <param name="outFormat" type="select" label="Output Format">
      <option value="sam">Sam</option>
      <option value="bam">Bam</option>
    </param>
    <param name="st" type="select" label="Sequencing Technology Used">
      <option value="454">454</option>
      <option value="illumina">Illumina</option>
      <option value="solid">Solid</option>
      <option value="sanger">Sanger</option>
      <option value="helicos">Helicos</option>
    </param>
    <conditional name="paired">
      <param name="kind" type="select" label="Is this library mate-paired?">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
      </param>
      <when value="single"/>
      <when value="paired">
        <param name="mfl" type="integer" value="200" label="Insert Size" help="the length between the paired reads"/>
        <param name="ls" type="integer" value="50" label="Realignment Window" help="Window size to realign mate pairs that are out of position. Large values slow down performance"/>
      </when>
    </conditional>
    <param name="mm" size="5" type="integer" value="6" label="Mismatches allowed" help="mismatches allowed per sequence"/>
    <param name="act" size="5" type="integer" value="35" label="Alignment Candidate Threshold" help="determines which hash regions will be aligned with Smith Waterman"/>
    <param name="bw" size="5" type="integer" value="19" label="Smith-Waterman band width"/>
    <param name="mhp" size="5" type="integer" value="100" label="Maximum # Of Positions Stored Per Seed" help="number of places in the reference the aligner will try to place a particular hash"/>
  </inputs>
  <outputs>
    <data format="sam" name="output">
      <change_format>
        <when input="outFormat" value="bam" format="bam" />
      </change_format>
      <actions>
        <conditional name="genomeSource.refGenomeSource">
          <when value="indexed">
            <action type="metadata" name="dbkey">
              <option type="from_data_table" name="mosaik_indexes" column="1">
                <filter type="param_value" column="0" value="#" compare="startswith" keep="False" />
                <filter type="param_value" ref="genomeSource.indexReference" column="0" />
              </option>
            </action>
          </when>
          <when value="history">
            <action type="metadata" name="dbkey">
              <option type="from_param" name="genomeSource.historyReference" param_attribute="dbkey" />
            </action>
          </when>
        </conditional>
      </actions>
   </data>
  </outputs>
  <tests>
    <test>
      <param name="refGenomeSource" value="history"/>
      <param name="historyReference" ftype="fasta" value="mosaik_test_ref.fasta"/>
      <param name="reads" ftype="fastq" value="mosaik_test_input.fastq"/>
      <param name="outFormat" value="sam"/>
      <param name="st" value="454"/>
      <param name="kind" value="single"/>
      <param name="mm" value="6"/>
      <param name="act" value="35"/>
      <param name="bw" value="19"/>
      <param name="mhp" value="100"/>
      <output name="output" file="mosaik_test_out.sam" compare="sim_size" delta="0"/>
    </test>
  </tests>
  <help>
This tool uses Mosaik to align reads to a reference sequence.
  </help>
</tool>