<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">pandas</requirement>
      <requirement type="package">mash</requirement>
      <requirement type="package">requests</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #if $jobtype.select == "asm"
        ln -s $jobtype.draft sample.fasta;  
      #else if $jobtype.select == "se"
        ln -s $jobtype.fastq1 sample_1.fastq;  
      #else if $jobtype.select == "pe"
        ln -s $jobtype.fastq1 sample_1.fastq;  
        ln -s $jobtype.fastq2 sample_2.fastq;  
      #end if

      $__tool_directory__/bin/ectyper
      #if $jobtype.select == "asm"
        -m 4
        -i sample.fasta
      #else if $jobtype.select == "se"
        -m 3
        -i sample_1.fastq
      #else if $jobtype.select == "pe"
        -m 2
        -i sample_1.fastq sample_2.fastq
      #end if
      -b $maptype.select;
      cat  ectyper_result*/ectyper_result.txt > results.txt; 

    ]]></command>
    <inputs>
      <conditional name="jobtype">
        <param name="select" type="select" label="Assembly or FASTQ Reads?">
          <option value="asm">Genome Assembly</option>
          <option value="se">Single-End Reads</option>
          <option value="pe">Paired-End Reads</option>
        </param>
        <when value="asm">
          <param name="draft" type="data" format="fasta" label="FASTA" />
        </when>
        <when value="se">
          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
        </when>
        <when value="pe">
          <param name="fastq1" type="data" format="fastq" label="FASTQ" />
          <param name="fastq2" type="data" format="fastq" label="FASTQ" />
        </when>
      </conditional>

      <conditional name="maptype">
        <param name="select" type="select" label="Algorithms for BWA mapping?">
          <option value="sam">sam</option>
          <option value="mem">mem</option>
        </param>
      </conditional>
    

    </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**

A fasta assembly

**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>