Mercurial > repos > charles_s_test > seqsero2

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author charles_s_test
date Thu, 30 Nov 2017 16:58:25 -0500
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1 <tool id="seq_sero_reads_multiple" name="SeqSero Batch - Paired-End Reads" version="0.1.0">
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2 <requirement type="package" version="1.69">biopython</requirement>
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3 <requirement type="package" >samtools</requirement>
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4 <description>Salmonella Serotype Prediction from Paired-End Reads</description>
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5 <command interpreter="python2.7">
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6 run_seqsero_batch_galaxy.py $input1 <!--$input2-->
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7 <!--test_bioblend.py $input1 $input2-->
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8 </command>
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9 <inputs>
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10 <param format="fastq" name="input1" multiple="true" type="data" label="Source file"/>
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11 <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
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12 </inputs>
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13 <outputs>
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14 <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
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15 <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
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16 </outputs>
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17 <help>
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18 This tool predicts Salmonella serotypes from shotgun WGS data.
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19 <description>
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20 xlink:type="simple"
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21 xlink:href="/nfs/sw/apps/galaxy/static/toolpages/seqsero/seqsero.html"
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22 xlink:show="SeqSero documentation"
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23 </description>
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24 </help>
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25 <citations>
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26 <citation type="bibtex">
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27 @Article{pmid25762776,
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28 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. ",
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29 Title="{{S}almonella serotype determination utilizing high-throughput genome sequencing data}",
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30 Journal="J. Clin. Microbiol.",
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31 Year="2015",
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32 Volume="53",
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33 Number="5",
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34 Pages="1685--1692",
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35 Month="May"
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36 }
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37 </citation>
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38 </citations>
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39 <stdio>
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40 <exit_code range="0:" level="warning"/>
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41 <regex match="Error:"/>
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42 </stdio>
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43 </tool>