<tool id="catchsequence" name="catchSequenceInfo" version="1.0.0">
  <description>catchSequenceInfo allows to get resistance/virulence/plasmids/mlst information from DNA sequences</description>
<requirements>
  <requirement type="package" version="1.0.1">abricate</requirement>
  <requirement type="package" version="2.19.0">mlst</requirement>
  <!--<requirement type="package" version="6.6.0">emboss</requirement>
  <requirement type="package" version="1.3.2">pandas</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')
        #set $named_input_files = ''
        #for $input_file in $input_files
            ## Add single quotes around each input file identifier
            #set $_input_file = "'{}'".format($input_file.element_identifier)
            ln -s '${input_file}' ${_input_file} && 
            #set $named_input_files = $named_input_files + ',' + $_input_file
        #end for

	
  	perl '$__tool_directory__/catchsequence.pl' $named_input_files -perc $percent -res $res -plas $plas -vf $vf > "$output"
	
       

]]></command>
 <!-- perl '$__tool_directory__/nucleScore.pl' $_input_file > "$output"  -->
 <!-- ./nuclescore.sh ${named_input_files} > "$output" -->

<inputs>
  <param type="data" name="input_files" format="fasta,fasta.gz,fasta.bz2,gbk,gbk.gz,gbk.bz2" multiple="true" label="Genome fasta files"/>

  <param name="percent" type="select" label="Percentage type:">
    <option value="ident">Identity</option>
    <option value="cov">Coverage</option>
  </param>

  <param name="res" type="text" area="false" value="90.00" label="ResFinder %: " />
  <param name="plas" type="text" area="false" value="90.00" label="PlasmidFinder %: " />
  <param name="vf" type="text" area="false" value="80.00" label="VFDB %: " />

</inputs>

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

<help>
catchSequenceInfo allows to get resistance/virulence/plasmids/mlst information from DNA sequences.

This tool uses ABRicate (https://github.com/tseemann/abricate) and MLST (https://github.com/tseemann/mlst) programs to get dedicated information from DNA sequences (such as resistance genes, plasmid genes, virulence genes, allele IDs and MLST number). 


</help>

<citations>
  <citation type="doi">10.1186/1471-2105-11-595</citation>
  <citation type="doi">10.1093/jac/dks261</citation>
  <citation type="doi">10.1128/AAC.02412-14</citation>
  <citation type="doi">10.1093/nar/gkv1239</citation>
</citations>

</tool>