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author charles_s_test
date Sun, 12 Nov 2017 02:26:17 -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 <description>Salmonella Serotype Prediction from Paired-End Reads</description>
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3 <requirements>
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4 <requirement type="package" version="1.69">biopython</requirement>
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5 <requirement type="package" version="0.5.9">bwa</requirement>
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6 <requirement type="package" version="1.3.1">samtools</requirement>
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7 <requirement type="package" version="2.5.0">blast</requirement>
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8 <requirement type="package" version="2.6.2">sra_toolkit</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="0:" level="warning"/>
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12 <regex match="Error:"/>
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13 </stdio>
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14 <command interpreter="python2.7">
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15 run_seqsero_batch_galaxy.py $input1 <!--$input2-->
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16 <!--test_bioblend.py $input1 $input2-->
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17 </command>
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18 <inputs>
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19 <param format="fastq" name="input1" multiple="true" type="data" label="Source file"/>
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20 <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
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21 </inputs>
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22 <outputs>
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23 <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
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24 <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <output name="text_file" file="Seqsero_result.txt" ftype="txt"/>
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29 </test>
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30 </tests>
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31 <help>
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32 This tool predicts Salmonella serotypes from shotgun WGS data.
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33
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34 Below is the link to the seqsero help
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35
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36 https://galaxy.ravencloudhpc.com/static/toolpages/seqsero/seqsero.html
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37
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38 </help>
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39 <citations>
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40 <citation type="bibtex">
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41 @Article{pmid25762776,
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42 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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43 Title="{{S}almonella serotype determination utilizing high-throughput genome sequencing data}",
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44 Journal="J. Clin. Microbiol.",
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45 Year="2015",
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46 Volume="53",
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47 Number="5",
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48 Pages="1685--1692",
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49 Month="May"
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50 }
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51 </citation>
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52 </citations>
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53 </tool>