<tool id="Resfinder" name="Resfinder" version="1">
  <description>
    Resfinder: Identifcation of acquired antibiotic resistance genes
  </description>
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  </requirements>
  <command detect_errors="exit_code"><![CDATA[
    python3 /home/galaxy/resfinder/run_resfinder.py -s "$s" -l "$l" -t "$t" --acquired --point -ifa ${input} -db_res /home/galaxy/resfinder/db_resfinder/ -db_point /home/galaxy/resfinder/db_pointfinder/ -o output && mv ./output/ResFinder_Resistance_gene_seq.fsa $resistance_genes
  ]]></command>
  <inputs>
    <param format="fasta" name="input" type="data" label="FASTA file : "/>
    <param name="s" type="select" label="Select the species:" help="*Chromosomal point mutation database exist">
      <option value="campylobacter">Campylobacter spp.*</option>
      <option value="campylobacter jejuni">Campylobacter jejuni*</option>
      <option value="campylobacter coli">Campylobacter coli*</option>
      <option value="escherichia coli">Escherichia coli*</option>
      <option value="salmonella">Salmonella spp.*</option>
      <option value="plasmodium falciparum">Plasmodium falciparum*</option>
      <option value="neisseria gonorrhoeae">Neisseria gonorrhoeae*</option>
      <option value="mycobacterium tuberculosis">Mycobacterium tuberculosis*</option>
      <option value="enterococcus faecalis">Enterococcus faecalis*</option>
      <option value="enterococcus faecium">Enterococcus faecium*</option>
      <option value="klebsiella">Klebsiella*</option>
      <option value="helicobacter pylori">Helicobacter pylori*</option>
      <option value="staphylococcus aureus">Staphylococcus aureus*</option>
      <option value="other">Other</option>
    </param>
    <param name="l" type="text" area="false" value="0.6" label="Minimum (breadth-of) coverage of ResFinder within the range 0-1:"/>
    <param name="t" type="text" value="0.8" area="false" label="Threshold for identity of ResFinder within the range 0-1:"/>
  </inputs> 
  <outputs>
	  <collection name="outputreport" type="list" label="${tool.name} on ${on_string}: Report files">
      <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" directory="./output" format="txt"/>
    </collection>
    <data format="fasta" name="resistance_genes" label="${tool.name} on ${on_string}: resistance genes"/>
  </outputs>
  <help><![CDATA[
    This tool allows to identify acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria (in FASTA format).
 
    BitBucket: https://bitbucket.org/genomicepidemiology/resfinder/src/master/  
  ]]></help>

  <citations>
    <citation type="doi">10.1093/jac/dkaa345</citation>
  </citations>
</tool>