Mercurial > repos > charles_s_test > seqsero

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author charles_s_test
date Sun, 12 Nov 2017 02:26:17 -0500
parents 8db411fab3e1
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1 <bookstore xmlns:xlink="http://www.w3.org/1999/xlink">
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2
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3 <tool id="seq_sero_reads_multiple" name="SeqSero Batch - Paired-End Reads" version="0.1.0">
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4 <requirement type="package" version="1.69">biopython</requirement>
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5 <requirement type="package" >samtools</requirement>
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6 <description>Salmonella Serotype Prediction from Paired-End Reads</description>
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7 <command interpreter="python2.7">
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8 run_seqsero_batch_galaxy.py $input1 <!--$input2-->
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9 <!--test_bioblend.py $input1 $input2-->
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10 </command>
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11 <inputs>
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12 <param format="fastq" name="input1" multiple="true" type="data" label="Source file"/>
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13 <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
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14 </inputs>
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15 <outputs>
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16 <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
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17 <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
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18 </outputs>
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19 <help>
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20 <!--This tool predicts Salmonella serotypes from shotgun WGS data.-->
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21 .._htmlFile: "/nfs/sw/apps/galaxy/static/toolpages/seqsero/seqsero.html"
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22 </help>
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23 <citations>
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24 <citation type="bibtex">
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25 @Article{pmid25762776,
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26 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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27 Title="{{S}almonella serotype determination utilizing high-throughput genome sequencing data}",
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28 Journal="J. Clin. Microbiol.",
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29 Year="2015",
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30 Volume="53",
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31 Number="5",
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32 Pages="1685--1692",
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33 Month="May"
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34 }
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35 </citation>
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36 </citations>
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37 <stdio>
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38 <exit_code range="0:" level="warning"/>
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39 <regex match="Error:"/>
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40 </stdio>
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41 </tool>