<tool id="seqsero_v2" name="seqsero_v2" version="2.0">
    <requirements>
      <requirement type="package" version="2.7">python</requirement>
      <requirement type="package">biopython</requirement>
      <requirement type="package">blast</requirement>
      <requirement type="package">samtools</requirement>
      <requirement type="package">sra-tools</requirement>
      <requirement type="package">bwa</requirement>
      <requirement type="package">spades</requirement>
      <requirement type="package">bedtools</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
     
        ln -s $fastq1 sample_1.fastq;  
        ln -s $fastq2 sample_2.fastq;  
 
  

      $__tool_directory__/SeqSero2.py
      -p $numofthr
      -i sample_1.fastq sample_2.fastq
      -b $maptype; 
      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="SeqSero Results" name="results" from_work_dir="results.txt"/>
    </outputs>
    <tests>
       <test>
         <output name="results" file="results.txt"/>
       </test>
    </tests>
    <help><![CDATA[
    
**Usage: SeqSero2.py** 

**Number of threads**

The range is 1 through 4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1

**Algorithms for BWA mapping**

'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
   
    ]]></help>
    <citations>
       <citation type="bibtex">
        @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
        title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
        journal={J Clin Microbiol}, publisher={ASM},
        author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
        year={2015}, month={Max},
        url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
       }</citation>
    </citations>

</tool>