<tool id="stringmlst" name="StringMLST" version="1.0.4">
  <description>k-mer tool for multilocus sequence typing</description>
  <requirements>
    <requirement type="package" version="2.1">stringmlst</requirement>
  </requirements>
  <stdio>
    <exit_code range="1:" />
  </stdio>
  <command><![CDATA[



  python $__tool_directory__/split_by_allele.py --alleles=$alleles --profiles=$scheme
  &&
  stringMLST.py --buildDB -c config.txt -k $kmer -P DB

  &&  
        #if $single_or_paired.type == "single"
        ln -s "$input_se" "$single_or_paired.input_se.element_identifier".fastq && 

        stringMLST.py
        --predict
        -1 "$single_or_paired.input_se.element_identifier".fastq
        -s 
        #elif $single_or_paired.type == "paired"
            ln -s  "$single_or_paired.forward_pe" "$single_or_paired.forward_pe.name"_1.fastq && ln -s  "$single_or_paired.reverse_pe" "$single_or_paired.forward_pe.name"_2.fastq &&
            stringMLST.py
            --predict
            -1 "$single_or_paired.forward_pe.name"_1.fastq -2 "$single_or_paired.forward_pe.name"_2.fastq
            -p
        #else
            ln -s "$single_or_paired.fastq_collection.forward" "$single_or_paired.fastq_collection.forward.name"_1.fastq && ln -s  "$single_or_paired.fastq_collection.reverse" "$single_or_paired.fastq_collection.forward.name"_2.fastq &&
            stringMLST.py
            --predict
            -1 "$single_or_paired.fastq_collection.forward.name"_1.fastq -2 "$single_or_paired.fastq_collection.forward.name"_2.fastq
            -p
        #end if
        -o $output
        -r 
        -P DB -k $kmer
  
  ]]></command>
  <inputs>
    <conditional name="single_or_paired">
      <param name="type" type="select" label="Read type">
        <option value="single">Single-end</option>
        <option value="paired">Paired-end</option>
        <option value="collection">Collection Paired-end</option>
      </param>
      <when value="single">
        <param name="input_se" type="data" format="fastqsanger" label="Single end read file(s)"/>
      </when>
      <when value="paired">
        <param name="forward_pe" type="data" format="fastqsanger" label="Forward paired-end read file"/>
        <param name="reverse_pe" type="data" format="fastqsanger" label="Reverse paired-end read file"/>
      </when>
      <when value="collection">
        <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger" collection_type="paired" />
      </when>
    </conditional>
    <param name="kmer" type="integer" label="K-mer to use" value="35" help="  Kmer length for which the db was created(Default k = 35)." />      
    <param name="scheme" type="data" format="tabular" label="ST definitions for MLST scheme"/>
    <param name="alleles" type="data" format="fasta" label="Fasta file of MLST alleles"/>
    
  </inputs>
  <outputs>
    <data format="tabular" name="output" label="Results"/>
    <data format="txt" name="log" label="Log" from_work_dir="DB.log"/>
    <data format="fastqsanger" name="reads" label='Reads' from_work_dir="*.fq" >

    </data>
  </outputs>
  <tests>
    <test>
      <param name="scheme" value="st.tabular" />
      <param name="alleles" value="st.fasta" />
      <param name="input_se" value="input.fastqsanger" />
      <output file="results.tsv" ftype="tabular" name="output" />
    </test>
  </tests>
  <help><![CDATA[
Original manual for command line available at http://jordan.biology.gatech.edu/page/software/stringmlst/stringMLST-useageDocumentation.pdf
]]>
  
  </help>
  <citations>
  </citations>
</tool>