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1 <tool id="seqsero_v2" name="SeqSero 2" version="2.0">
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2 <description>Salmonella serotype prediction</description>
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3 <requirements>
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4 <requirement type="package" version="2.7.10">python</requirement>
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5 <requirement type="package" version="1.60">biopython</requirement>
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6 <requirement type="package" version="2.2.31">blast</requirement>
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7 <requirement type="package" version="1.9">samtools</requirement>
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8 <requirement type="package" version="2.6.2">sra-tools</requirement>
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9 <requirement type="package" version="0.7.17">bwa</requirement>
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10 <requirement type="package" version="3.9.0">spades</requirement>
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11 <requirement type="package" version="2.27.1">bedtools</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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14 #if $reads.reads_select == 'history'
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15 #set name = $reads.forward.name.split('_')[0]
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16 #set forward = $reads.forward
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17 #set reverse = $reads.reverse
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18 #else
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19 #set name = $reads.coll.name
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20 #set forward = $reads.coll.forward
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21 #set reverse = $reads.coll.reverse
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22 #end if
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23 #if forward.is_of_type('fastq.gz', 'fastqsanger.gz')
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24 gunzip -c $forward > forward.fastq;
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25 #set forward = './forward.fastq'
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26 #end if
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27 #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
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28 gunzip -c $reverse > reverse.fastq;
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29 #set reverse = './reverse.fastq'
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30 #end if
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31 ln -s forward.fastq ${name}_1.fastq;
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32 ln -s reverse.fastq ${name}_2.fastq;
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33 $__tool_directory__/SeqSero2.py
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34 -p \${GALAXY_SLOTS:-4}
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35 -i ${name}_1.fastq ${name}_2.fastq
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36 -b $maptype &&
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37 cat SeqSero_result*/Seqsero_result.tsv > results.tsv
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38
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39 ]]></command>
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40 <inputs>
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41
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42
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43 <conditional name="reads">
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44 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
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45 <option value="collection">Paired collection from your history</option>
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46 <option value="history">Two FASTQ datasets from your history</option>
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47 </param>
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48 <when value="collection">
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49 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
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50 </when>
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51 <when value="history">
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52 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
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53 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
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54 </when>
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55 </conditional>
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56
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57 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
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58 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
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59 <!-- <param name="numofthr" type="select" label="Number of threads">
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60 <option value="1">1</option>
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61 <option value="2">2</option>
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62 <option value="3">3</option>
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63 <option value="4">4</option> -->
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64 <!-- </param> -->
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65 <param name="maptype" type="select" label="Algorithms for BWA mapping?">
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66 <option value="mem">mem</option>
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67 <option value="sam">sam</option>
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68 </param>
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69
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70
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71 </inputs>
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72 <outputs>
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73 <data format="tsv" label="SeqSero Results" name="results" from_work_dir="results.tsv"/>
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74 </outputs>
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75 <tests>
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76 <test>
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77 <param name="reads_select" value="history" />
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78 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
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79 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
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80 </test>
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81 <test>
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82 <param name="reads_select" value="collection" />
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83 <param name="coll">
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84 <collection type="paired">
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85 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
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86 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
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87 </collection>
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88 </param>
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89 </test>
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90 </tests>
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91 <help><![CDATA[
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92
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93 **Usage: SeqSero2.py**
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94
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95 **Algorithms for BWA mapping**
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96
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97 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
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98
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99 ]]></help>
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100 <citations>
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101 <citation type="bibtex">
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102 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
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103 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
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104 journal={J Clin Microbiol}, publisher={ASM},
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105 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
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106 year={2015}, month={Max},
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107 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
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108 }</citation>
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109 </citations>
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110
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111 </tool>
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