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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 <description>Salmonella Serotype Prediction from Paired-End Reads</description>
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3 <requirements>
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4 <requirement type="package" version="1.67">biopython</requirement>
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5 <requirement type="package" version="0.1.16" >samtools</requirement>
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6 <requirement type="package" version="0.7.17" >bwa</requirement>
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7 <requirement type="package" version="2.5.0">blast</requirement>
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8 <requirement type="package" version="2.8.1">sra-tools</requirement>
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9 </requirements>
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10
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11 <stdio>
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12 <exit_code range="0:" level="warning"/>
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13 <regex match="Error:"/>
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14 </stdio>
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15 <command interpreter="python2.7">
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16
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17 $__tool_directory__/run_seqsero.py $input1 $__tool_directory__/
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18
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19 </command>
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20 <inputs>
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21 <param format="fastq,fastqsanger" name="input1" multiple="true" type="data" label="Source file"/>
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22 <!--<param format="fastq" name="input2" multiple="true" type="data" label="Source file"/>-->
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23 </inputs>
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24 <outputs>
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25 <data name="html_file" format="html" from_work_dir="Seqsero_result.html"/>
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26 <data name="text_file" format="txt" from_work_dir="Seqsero_result.txt"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <output name="text_txt" file="Seqsero_result.txt"/>
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31 </test>
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32 </tests>
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33 <help>
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34 **This tool predicts Salmonella serotypes from shotgun WGS data.**
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35
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36
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37 **SeqSero Documentation**
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38
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39 **Log in:**
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40  A username and password should have been emailed to you – change your password after logging in the first time.
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41
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42 **Creating and naming a history (histories in Galaxy are what datasets are associated with):**
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43  Click on the cog in the upper right corner and choose “create new” from the dropdown menu. To name your history, click on the current name (“unnamed history”) type a new name and hit return.
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44
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45 **Uploading data:**
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46  Click on the disk with the up arrow in the upper left region. Click on choose local file and navigate to the file. Select the paired end read files to be used and click open. Alternatively, files can be dragged into the box. After the files of interest have been selected click start to upload them to the Galaxy server.
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47
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48 **Running SeqSero:**
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49  In the left pane, click on “FDA tools” then “SeqSero Batch – Paired-End Reads.” Select the pairs of sequencing runs of interest and click on “Execute” in the main pane.
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50
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51 **Share a dataset:**
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52  Make sure your current library contains the data you want to share. Click on “Shared Data” from the top. Then choose “Data Libraries” from the dropdown. If you want the data to have its own folder, click on “+ new library” and give it a name. Choose the library to which you want to add the data and click on “+ data (page icon)”. Select the datasets you want to share and click “Add”. Or click on the cog in the upper right and select copy datasets from the dropdown.
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53
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54 **Import dataset into current history:**
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55  Go to “Shared Data” → “Data Libraries”. Select the relevant library and select the data of interest. Click on “to History”. Select the correct history from the dropdown and click import.
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56
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57 </help>
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58
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59 <citations>
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60 <citation type="bibtex">
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61 @Article{pmid25762776,
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62 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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63 Title="{{S}almonella serotype determination utilizing high-throughput genome sequencing data}",
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64 Journal="J. Clin. Microbiol.",
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65 Year="2015",
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66 Volume="53",
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67 Number="5",
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68 Pages="1685--1692",
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69 Month="May"
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70 }
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71 </citation>
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72 </citations>
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73
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74 </tool>