<tool id="resfinder" name="ResFinder" version="4.0">
  <description>identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria.</description>

<requirements>
  <requirement type="package" version="0.8.9">tabulate</requirement>
  <requirement type="package" version="1.79">biopython</requirement>
  <requirement type="package" version="1.5.6">cgecore</requirement>
  <requirement type="package" version="3.1.24">gitpython</requirement>
  <requirement type="package" version="2.8.2">python-dateutil</requirement>
  <requirement type="package" version="2.34.1">git</requirement>
  <requirement type="package" version="3.0.5">gcg</requirement>
</requirements>

 <command detect_errors="aggressive"><![CDATA[
        #import re
        ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
        ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
        ## Add single quotes around each input file identifier
        #set $_input_file = "'{}'".format($input.element_identifier)
        ln -s '${input}' ${_input_file} && 
		
	$__tool_directory__/resfinder/run_resfinder.py -s "$s" -l 0.6 -t 0.8 --acquired --point -ifa $_input_file -db_res $__tool_directory__/resfinder/db_resfinder/ -db_point $__tool_directory__/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="${tool.name}: Report files">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" directory="./output" format="txt"/>
  </collection>

  <data format="fasta" name="resistance_genes" label="${tool.name}: 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>