<tool id="rtg_format_fasta" name="Format FASTA">
  <description>to SDF with rtg format</description>
  <command interpreter="bash">galaxy-rtg-wrapper.sh format 
#if $paired.sPaired == "paired":
-l $paired.input1
-r $paired.input2 
#else:
$paired.input1
#end if
#if str($protein) == "true":
-p
#end if
-o ${output.extra_files_path} >$output</command>
  <inputs>
    <conditional name="paired">
      <param name="sPaired" type="select" label="Are you formatting paired-end reads?">
        <option value="single">Non-read data or single-end</option>
        <option value="paired">Paired-end</option>
      </param>
      <when value="single">
        <param name="input1" type="data" format="fasta" label="Source FASTA file"/>
      </when>
      <when value="paired">
        <param name="input1" type="data" format="fasta" label="First of pair FASTA file"/>
        <param name="input2" type="data" format="fasta" label="Second of pairFASTA file"/>
      </when>
    </conditional>
    <param name="protein" type="select" label="Input consists of protein">
      <option value="false" selected="true">False</option>	
      <option value="true">True</option>	
    </param>
  </inputs>
  <outputs>
    <data format="rtg_sdf" name="output" />
  </outputs>

  <help>
This tool formats a FASTA file to RTG SDF.
  </help>

</tool>