<tool id="novocraft_wrapper" name="Novocraft" version="3.00.02">
 <description>maps query reads onto the reference sequences</description>
  <command interpreter="python">
   novocraft_wrapper.py 
   ## Parameters
      --settings=$params.settingsType
   #if $params.settingsType == "full":
  	--align=${params.t}
   	--open=${params.g}
   	--extend=${params.x}
   	--trunc=${params.n}
   	--kmer=${params.k}
   	--step=${params.s}
   	--qual=${params.l}
   	--repe=${params.m}
   	--hclip=${params.H}
   	--pam=$params.pairedEnd
   	--sd=${params.d}
   	--insert=${params.i}
   #end if

   #if $genomeSource.refGenomeSource == "history":
        ##build index on the fly
        --refer="${genomeSource.refFile}"
        ##--dbkey=$dbkey
      #else:
        ##use precomputed indexes
        --ref1="${genomeSource.indices.fields.path}"
        ##--do_not_build_index
   #end if

   ## input file(s)
      --input1=$paired.input1
   #if $paired.sPaired == "paired":
        --input2=$paired.input2
   #end if

   ## Outputs.
   --output=$output

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

      <when value="history">
        <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
      </when>
    </conditional>

    <conditional name="paired">
      <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="input1" type="data" format="fastq" label="FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
      </when>
      <when value="paired">
        <param name="input1" type="data" format="fastq" label="Forward FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
        <param name="input2" type="data" format="fastq" label="Reverse FASTQ file" help="FASTQ with Sanger-scaled quality values (fastqsanger)" />
      </when>
    </conditional>
     <conditional name="params">
            <param name="settingsType" type="select" label="Parameter Settings" help="You can use the default settings or set custom values for the parameters.">
              <option value="preSet">Use Defaults</option>
              <option value="full">Full parameter list</option>
            </param>
            <when value="preSet" />
            <!-- Full/advanced parameters. -->
            <when value="full">
                 <!-- Indexing parameters -->
                  <param name="k" type="text" value="13" label="k-mer length for the index" />
                  <param name="s" type="text"  value="2" label="step size for the index" /> 
                  <!-- Alignment Scoring -->
                 <param name="t" type="text" value="99" label="maximum alignment score" />
                 <param name="g" type="text"  value="40" label="Gap opening penalty" /> 
                 <param name="x" type="text" value="6" label="Gap extending penalty" />
                 <!--  Read preprocessing -->
                 <param name="n" type="text" value="80" label="Truncate read to specified length" />
                 <!--  Quality control -->
                 <param name="l" type="text" value="50" label="minimum number of good quality bases" />
                 <param name="m" type="text"  value="20" label="Repeat filter" /> 
                 <param name="H" type="text" value="2" label="Hard clip 3' bases" />
                 <param name="pairedEnd" type="select" label="Paired End" >
              		<option value="mp">MP</option>
              		<option value="pe">PE</option>
              		<option value="pp">++</option>
              		<option value="pn">+-</option>
              		<option value="np">-+</option>
          	 </param>

          	 <param name="i" type="text" value="200" label="Insert size" />
          	 <param name="d" type="text" value="50" label="standard deviation" />
                 
           </when>  <!-- full -->
      </conditional>  <!-- params -->


</inputs>
   <outputs>
    	<data format="txt" name="output" label="${tool.name} on ${on_string}:"/>
   </outputs>
   <help>

**Novoalign**

Novoalign is highly accurate program for mapping next-generation sequencing reads to a reference database. (http://www.novocraft.com/). Selected parameters used here are listed here.

------

**Indexing usage**

novoindex options indexfile sequencefiles

------

**Options - Description**

-­k 99

k­mer length to be used for the index. Novoindex will select appropriate values if either of these is not specified. Default value is log4(N/20s) where N is genome size and s step size.

-s 9

step size for the index. Typical values are from 1 to 3, usually defaults to 1 or 2.  Genomes larger than 4Gbp can be indexed using a stepsize > 1, the requirement is N/s less than 4G.

------

**Alignment usage**

 novoalign options

------

**Options - Description**

-d dbname    
  
Full pathname of indexed reference sequence from novoindex

-f read1 read2    

Filenames for the read sequences for Side 1 and 2.

-­t 99

Sets absolute threshold or highest alignment score acceptable for the best alignment.

-g 99

Sets the gap opening penalty. Default 40

-­x 99

Sets the gap extend penalty. Default 6

-­l 99

Sets the minimum number of good quality bases for a read. 

-­H [99]

Hard clips 3' bases with quality &lt;=[99] from reads before aligning them.



</help>

</tool>