<tool id="kleboratetool" name="Kleborate" version="0.1.0">
  <description>Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae</description>
 <requirements>
  <requirement type="package" version="0.7.3">kaptive</requirement>
 <requirement type="package" version="2.0.4">kleborate</requirement>
</requirements>

  <command>kleborate -a `echo $input | tr ',' ' '` $r $kaptive_k $kaptive_o -o $output </command>
 
  <inputs>
	  <param format="fasta" name="input" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/>
	 
	  <param name="r" type="select" label="Turn on resistance genes screening (default: no resistance gene screening):">
            <option value="">no</option>
            <option value="-r">yes</option>
          </param>

          <param name="kaptive_k" type="select" label="Turn on Kaptive screening of K loci (default: do not run Kaptive for K loci):">
	    <option value="">no</option>
	    <option value="--kaptive_k">yes</option>
          </param>
	
          <param name="kaptive_o" type="select" label="Turn on Kaptive screening of O loci (default: do not run Kaptive for O loci):">
            <option value="">no</option>
            <option value="--kaptive_o">yes</option>
    </param> 
	   
 </inputs>

 <outputs>	 
    <data format="tabular" name="output" />
 </outputs>

 <tests>
    <test>
	    <param name="input" value="KP011_S63.scfd.fasta " />
	    <param name="input" value="KP012_S64.scfd.fasta " />
        <param name="r" value="-r"/>
	<param name="kaptive_k" value="--kaptive_k"/>
	<param name="kaptive_o" value=""/>
        <output name="output" file="Kleborate_results.txt" />
    </test>
</tests>

  <help>
For full documentation, please go to the Kleborate wiki (https://github.com/katholt/Kleborate/wiki)
  </help>
  <citations>
	  <citation type="doi">10.1101/2020.12.14.422303</citation>
	        </citations> 
</tool>