<tool id="find_motif" name="findMotif" version="1.0.0">
  <description>Find specified motif in sequence</description>
  <command>/steno-internal/projects/galaxy-test/galaxy-dist/tools/findMotifs/findMotif -motif="$motif" "$input1" 
  #if str( $options_type.options_type_selector ) == "advanced":
  -chr="${options_type.chr}" 
  -strand="${options_type.strand} 
  "${options_type.wigOutput}" 
  #end if
  > "$output"
  </command>
  <inputs>
    <param format="fasta" name="input1" type="data" label="Sequences"/>
    <param name="motif" type="text" value="acgt" size="17" />
      
      <conditional name="options_type">
        <param name="options_type_selector" type="select" label="Options Configuration">
          <option value="basic" selected="true">Basic</option>
          <option value="advanced">Advanced</option>
        </param>
        <when value="basic">
          <!-- do nothing here -->
        </when>
        <when value="advanced">
      
        <param name="chr" size="6" type="integer" value="1" label="Process only this chr from the sequence"/>
	<param name="strand" type="select" label="Limit to only one strand">
	  <option value="+">+</option>
          <option value="-">-</option>
	</param>
	<param name="wigOutput" label="Output wiggle data format instead of bed file" type="boolean" truevalue="-wigOutput" falsevalue="" checked="False"/>
        </when>
      </conditional>
  </inputs>
  <outputs>
    <data format="bed" name="output" label="${tool.name} on ${on_string} (bed)"/>
  </outputs>

  <tests>
    <test>
      <param name="input1" value="find_motif_input.fa"/>
      <output name="output" file="find_motif__output.bed"/>
    </test>
  </tests>

  <help>
Find specified motif in a sequence from a FASTA file.
  </help>

</tool>