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<tool id="seq_sero_reads_multiple" name="SeqSero Batch - Paired-End Reads" version="0.1.0">
  <description>Salmonella Serotype Prediction from Paired-End Reads</description>  
<requirements>
	<requirement type="package" version="1.69">biopython</requirement>
        <requirement type="package" version="0.5.9">bwa</requirement>
        <requirement type="package" version="1.3.1">samtools</requirement>
        <requirement type="package" version="2.5.0">blast</requirement>
        <requirement type="package" version="2.6.2">sra_toolkit</requirement>
  </requirements>
       <stdio>
                <exit_code range="0:" level="warning"/>
                <regex match="Error:"/>
        </stdio>  
      <command interpreter="python2.7">
                run_seqsero_batch_galaxy.py $input1 <!--$input2-->
                <!--test_bioblend.py $input1 $input2-->
        </command>
        <inputs>
                <param format="fastq" name="input1" multiple="true" type="data" label="Source file"/>
                <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
        </inputs>
        <outputs>
                <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
                <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
        </outputs>
 	<tests>
        <test>
            <output  name="text_file" file="Seqsero_result.txt" ftype="txt"/>
 	</test>
    	</tests>
	<help>
               This tool predicts Salmonella serotypes from shotgun WGS data.

          	Below is the link to the seqsero help

               https://galaxy.ravencloudhpc.com/static/toolpages/seqsero/seqsero.html

        </help>
     <citations>
          <citation type="bibtex"> 
          @Article{pmid25762776,
               Author="Zhang, S.  and Yin, Y.  and Jones, M. B.  and Zhang, Z.  and Deatherage Kaiser, B. L.  and Dinsmore, B. A.  and Fitzgerald, C.  and Fields, P. I.  and Deng, X. ",
                  Title="{{S}almonella serotype determination utilizing high-throughput genome sequencing data}",
                  Journal="J. Clin. Microbiol.",
                  Year="2015",
                  Volume="53",
                  Number="5",
                  Pages="1685--1692",
                  Month="May"
          }
          </citation>
     </citations>
</tool>