<tool id="FindNMers" name="Find NMers" version="1.0.0">
  <description>in a DNA sequence</description>
  <command interpreter="sh">galaxyToolRunner.sh dna.FindNMers -i 
    #if $refGenomeSource.genomeSource == "history":
      $refGenomeSource.ownFile
    #else
      ${refGenomeSource.index.fields.path}
    #end if
	-m $mismatches -n $nmer $rc -o $output
  </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 index?" help="Built-ins were indexed using default options">
        <option value="indexed">Use a built-in index</option>
        <option value="history">Use one from the history</option>
      </param>
      <when value="indexed">
        <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
          <options from_data_table="sam_fa_indexes">
            <filter type="sort_by" column="1" />
            <validator type="no_options" message="No indexes are available" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
      </when>  <!-- history -->
    </conditional>  <!-- refGenomeSource -->
    
    <param name="nmer" type="text" optional="false" label="NMer to search for" />
    <param name="mismatches" type="integer" value="0" label="Number of allowed mismatches (Hamming distance)" />
    <param name="rc" type="boolean" checked="true" truevalue="--rc" falsevalue="" label="Search reverse-complement as well" />
  </inputs>
  <outputs>
      <data format="bed" name="output"/>
  </outputs>
  <tests>
    <test>
      <param name="genomeSource" value="history"/>
      <param name="ownFile" value="test.fasta"/>
      <param name="property" value="Twist"/>
      <param name="N" value="false"/>
      <output name="output" file="twist.wig"/>
  	</test>
	</tests>
  
  <help>

This tool will find all matches of a given NMer in a DNA sequence. Sequences may be provided in FASTA format or selected from available reference genomes. Mismatches are allowed, but not insertions/deletions. The output is a Bed file with the locations of matches in the reference sequence.

  </help>
</tool>