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1 <tool id="shigatyper" name="ShigaTyper" version="1.0.5">
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2 <description>Shigella genoserotyping</description>
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3 <requirements>
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4 <requirement type="package" version="1.0.5">shigatyper</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #if $reads.reads_select == 'collection'
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8 #set forward=$reads.coll.forward
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9 #set reverse=$reads.coll.reverse
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10 #set name=$reads.coll.name
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11 #else
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12 #set name=$reads.coll.forward.name.split('_')[0]
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13 #end if
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14
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15 shigatyper -n "$name" "$forward" "$reverse" -vv >
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16
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17 #if $reads.reads_select == 'collection'
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18 ${serotype_from_collection}
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19 #else
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20 ${serotype_from_history}
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21 #end if
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22 ]]></command>
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23 <inputs>
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24 <conditional name="reads">
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25 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
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26 <option value="collection">Paired collection from your history</option>
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27 <option value="history">Two FASTQ datasets from your history</option>
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28 </param>
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29 <when value="collection">
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30 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
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31 </when>
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32 <when value="history">
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33 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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34 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
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35 </when>
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36 </conditional>
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37 </inputs>
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38 <outputs>
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39 <data label="${reads.coll.name} Shigella serotype determination" name="serotype_from_collection" format="sam">
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40 <filter>reads['reads_select'] == 'collection'</filter>
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41 </data>
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42 <data label="${reads.forward.name.split('_')[0]} Shigella serotype determination" name="serotype_from_history" format="sam">
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43 <filter>reads['reads_select'] == 'history'</filter>
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44 </data>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="reads_select" value="history" />
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49 <param name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz"/>
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50 <param name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz"/>
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51 <output name="serotype_from_history" file="output.tabular"/>
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52 </test>
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53 <test>
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54 <param name="reads_select" value="collection" />
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55 <param name="coll">
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56 <collection type="paired">
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57 <element name="forward" value="CFSAN029786_S10_L001_R1_001.fastq.gz" ftype="fastqsanger.gz" />
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58 <element name="reverse" value="CFSAN029786_S10_L001_R2_001.fastq.gz" ftype="fastqsanger.gz" />
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59 </collection>
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60 </param>
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61 <output name="serotype_from_collection" value="output.tabular" />
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65 usage: shigatyper [-h] [-n SAMPLE_NAME] [--verbose] [--version] read1 read2
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66
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67 positional arguments:
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68 read1
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69 read2
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70
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71
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72 ]]></help>
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73 <citations>
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74 <citation type="bibtex">
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75 @misc{githubshigatyper,
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76 author = Wu Y1, Lau HK, Lee T, Lau DK, Payne J.
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77 year = 2019,
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78 title = In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification,
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79 publisher = AEM,
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80 journal = Appl Environ Microbiol. ,
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81 url = https://www.ncbi.nlm.nih.gov/pubmed/30709819,
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82 }</citation>
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83 </citations>
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84 </tool> |
