view seqsero.xml.2 @ 1:8cd7fc65c3a7 draft

planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty

<bookstore xmlns:xlink="http://www.w3.org/1999/xlink">

<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.-->
               .._htmlFile: "/nfs/sw/apps/galaxy/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>
        <stdio>
                <exit_code range="0:" level="warning"/>
                <regex match="Error:"/>
        </stdio>
</tool>