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<tool id="seq_sero_reads_multiple" name="SeqSero Batch - Paired-End Reads" version="0.1.0">
        <requirement type="package" version="1.69">biopython</requirement>
        <requirement type="package" >samtools</requirement>
        <description>Salmonella Serotype Prediction from Paired-End Reads</description>
        <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>
        <help>
               This tool predicts Salmonella serotypes from shotgun WGS data.
          <description>
               xlink:type="simple"
               xlink:href="/nfs/sw/apps/galaxy/static/toolpages/seqsero/seqsero.html"
               xlink:show="SeqSero documentation"
          </description>
        </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>
        <stdio>
                <exit_code range="0:" level="warning"/>
                <regex match="Error:"/>
        </stdio>
</tool>