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author cstrittmatter
date Thu, 21 Dec 2017 12:48:10 -0500
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1 <tool id="seqsero_v2" name="seqsero_v2" version="2.0">
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2 <requirements>
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3 <requirement type="package" version="2.7">python</requirement>
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4 <requirement type="package">biopython</requirement>
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5 <requirement type="package">blast</requirement>
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6 <requirement type="package">samtools</requirement>
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7 <requirement type="package">sra-tools</requirement>
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8 <requirement type="package">bwa</requirement>
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9 <requirement type="package">spades</requirement>
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10 <requirement type="package">bedtools</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13
1
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14 ln -s $fastq1 sample_1.fastq;
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15 ln -s $fastq2 sample_2.fastq;
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16
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17 $__tool_directory__/SeqSero2.py
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18 -p $numofthr
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19 -i sample_1.fastq sample_2.fastq
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20 -b $maptype;
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21 cat SeqSero_result*/Seqsero_result.txt > results.txt;
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22
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23 ]]></command>
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24 <inputs>
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29 <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
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30 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" />
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31 <param name="numofthr" type="select" label="Number of threads">
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32 <option value="1">1</option>
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33 <option value="2">2</option>
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34 <option value="3">3</option>
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35 <option value="4">4</option>
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36 </param>
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37 <param name="maptype" type="select" label="Algorithms for BWA mapping?">
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38 <option value="mem">mem</option>
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39 <option value="sam">sam</option>
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40 </param>
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41
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42
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43 </inputs>
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44 <outputs>
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45 <data format="txt" label="SeqSero Results" name="results" from_work_dir="results.txt"/>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <output name="results" file="results.txt"/>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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53
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54 **Usage: SeqSero2.py**
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55
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56 **Number of threads**
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57
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58 The range is 1 through 4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1
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59
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60 **Algorithms for BWA mapping**
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61
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62 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
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63
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64 ]]></help>
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65 <citations>
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66 <citation type="bibtex">
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67 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
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68 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
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69 journal={J Clin Microbiol}, publisher={ASM},
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70 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
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71 year={2015}, month={Max},
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72 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
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73 }</citation>
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74 </citations>
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75
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76 </tool>