<tool id="smalt_index" name="smalt index" version="1.2.0">
  <description>Index a reference </description>
  <requirements>
    <requirement type="package" version="0.7.6">smalt</requirement>
  </requirements>
   <stdio>
    <exit_code range="1:"   level="fatal"   description="Unknown error" />
  </stdio>
 <command>
    smalt index 
    #if $k:
    -k "$k"
    #end if
    
    #if $s:
    -s "$s"
    #end if
    'temp' "$reference"
  </command>
  <inputs>
    <param name="reference" type="data" format="fasta" label="Fasta reference file"/>
    <param name="k" type="integer" value="13" label="K-mer size" help="Specifies the word length. [wordlen] is an integer within the limits. between 3 and 20. The default word length is 13" max="20" min="3"/>
    <param name="s" type="integer" optional="true" label="Step size" help="Specifies how many bases are skipped between indexed words."/>
  </inputs>
  <outputs>
    <data name="output" label="SMI" from_work_dir="temp.smi" format="binary"/>
    <data name="output2" label="SMA" from_work_dir="temp.sma" format="binary"/>
  </outputs>
  <tests>
    <test>
      <param name="reference" value="ref.fasta"/>
      <output name="output" file="output.smi"/>
      <output name="output2" file="output.sma"/> 
    </test>    
  </tests>
  <help>

**What it does**

Generates an index of k-mer words for the genomic reference sequences. The words are of fixed length &#060;wordlen&#062; and are sampled at equidistant steps &#060;stepsiz&#062; bases apart. The reference sequences are provided in a single file &#060;reference_file&#062; in FASTA or FASTQ format. Two binary files are output. The file &#060;index_name&#062;.sma contains the  reference sequences in compressed form. The file &#060;index_name&#062;.smi contains the k-mer word index.


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Please cite the website "http://www.sanger.ac.uk/resources/software/smalt/".
    
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  -k &#060;wordlen&#062;
     Specifies the word length. &#060;wordlen&#062; is an integer within the limits
     3 &#060; wordlen &#060;= 20. The default word length is 13.

  -s &#060;stepsiz&#062;
     Specifies how many bases are skipped between indexed words. With '-s 1'
     every k-mer word along the reference sequences is indexed. With '-s 2'
     every other word is indexed etc. By default the step size is set equal
     to the word length (tiling words).

    
  </help>
</tool>