<tool id="ectyper" name="ectyper" version="2.0">
    <requirements>
      <requirement type="package" version="3.6.3">python</requirement>
      <requirement type="package">biopython</requirement>
      <requirement type="package">blast</requirement>
      <requirement type="package">samtools</requirement>
      <requirement type="package">bcftools</requirement>
      <requirement type="package">bowtie</requirement>
      <requirement type="package">spades</requirement>
      <requirement type="package">seqtk</requirement>
#      <requirement type="package">mash</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
     
      ln -s $fasta1 sample_1.fastq;  
      ln -s $fastq2 sample_2.fastq;  

      $__tool_directory__/ectyper.py
      -i ecoliA.fasta for a single file
      -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna for multiple files
      -i ecoli_folder for a folder
      -i ecoli_folder for a folder
      -d PERCENTIDENTITY
      -l PERCENTLENGTH
      -o OUTPUT; 
      cat  SeqSero_result*/Seqsero_result.txt > results.txt; 

    ]]></command>
    <inputs>
          <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
          <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" />
          <param name="numofthr" type="select" label="Number of threads">
          <option value="1">1</option>
          <option value="2">2</option>
          <option value="3">3</option>
          <option value="4">4</option>
        </param>
        <param name="maptype" type="select" label="Algorithms for BWA mapping?">
          <option value="mem">mem</option>
          <option value="sam">sam</option>
        </param>
    

    </inputs>
    <outputs>
      <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/>
    </outputs>
    <tests>
       <test>
         <output name="results" file="results.txt"/>
       </test>
    </tests>
    <help><![CDATA[
    
**Usage: ectyper**

**INPUT**

Location of new file(s). Can be a single file or a directory

**PERCENTIDENTITY**

Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.

**PERCENTLENGTH**

Percentage of length wanted to use against the database. From 0 to 100, default is 50%.

**verify**

Enable E. Coli. verification

**species**

Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time.

**OUTPUT**
Directory location of output files.
    ]]></help>
</tool>