<tool id="seqsero_v1" name="seqsero_v1" version="1.0">
    <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>
    </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__/SeqSero.py
      #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 ample_2.fastq
      #end if
      -b $maptype.select 
      ; cat  SeqSero_result*/Seqsero_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="SeqSero Results" name="results" from_work_dir="results.txt"/>
    </outputs>
    <help><![CDATA[

    ]]></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>