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1 <tool id="seqsero_v1" name="seqsero_v1" version="1.0">
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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 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #if $jobtype.select == "asm"
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12 ln -s $jobtype.draft sample.fasta;
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13 #else if $jobtype.select == "se"
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14 ln -s $jobtype.fastq1 sample_1.fastq;
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15 #else if $jobtype.select == "pe"
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16 ln -s $jobtype.fastq1 sample_1.fastq;
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17 ln -s $jobtype.fastq2 sample_2.fastq;
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18 #end if
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19
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20 $__tool_directory__/SeqSero.py
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21 #if $jobtype.select == "asm"
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22 -m 4
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23 -i sample.fasta
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24 #else if $jobtype.select == "se"
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25 -m 3
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26 -i sample_1.fastq
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27 #else if $jobtype.select == "pe"
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28 -m 2
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29 -i sample_1.fastq sample_2.fastq
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30 #end if
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31 -b $maptype.select
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32 ; cat SeqSero_result*/Seqsero_result.txt > results.txt;
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33
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34 ]]></command>
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35 <inputs>
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36 <conditional name="jobtype">
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37 <param name="select" type="select" label="Assembly or FASTQ Reads?">
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38 <option value="asm">Genome Assembly</option>
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39 <option value="se">Single-End Reads</option>
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40 <option value="pe">Paired-End Reads</option>
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41 </param>
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42 <when value="asm">
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43 <param name="draft" type="data" format="fasta" label="FASTA" />
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44 </when>
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45 <when value="se">
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46 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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47 </when>
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48 <when value="pe">
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49 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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50 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
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51 </when>
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52 </conditional>
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53
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54 <conditional name="maptype">
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55 <param name="select" type="select" label="Algorithms for BWA mapping?">
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56 <option value="sam">sam</option>
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57 <option value="mem">mem</option>
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58 </param>
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59 </conditional>
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60
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61 </inputs>
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62 <outputs>
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63 <data format="txt" label="SeqSero Results" name="results" from_work_dir="results.txt"/>
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64 </outputs>
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65 <help><![CDATA[
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66
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67 ]]></help>
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68 <citations>
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69 <citation type="bibtex">
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70 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
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71 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
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72 journal={J Clin Microbiol}, publisher={ASM},
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73 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
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74 year={2015}, month={Max},
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75 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
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76 }</citation>
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77 </citations>
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78
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79 </tool>
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