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1 <tool id="ectyper" name="ectyper" version="2.0">
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2 <requirements>
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3 <requirement type="package" version="3.6.3">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">bcftools</requirement>
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8 <requirement type="package">bowtie</requirement>
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9 <requirement type="package">spades</requirement>
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10 <requirement type="package">seqtk</requirement>
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11 # <requirement type="package">mash</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
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1
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14 #if $jobtype.select == "asm"
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15 ln -s $jobtype.draft sample.fasta;
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16 #else if $jobtype.select == "se"
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17 ln -s $jobtype.fastq1 sample_1.fastq;
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18 #else if $jobtype.select == "pe"
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19 ln -s $jobtype.fastq1 sample_1.fastq;
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20 ln -s $jobtype.fastq2 sample_2.fastq;
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21 #end if
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0
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22
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23 $__tool_directory__/ectyper.py
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24 #if $jobtype.select == "asm"
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25 -m 4
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26 -i sample.fasta
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27 #else if $jobtype.select == "se"
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28 -m 3
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29 -i sample_1.fastq
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30 #else if $jobtype.select == "pe"
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31 -m 2
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32 -i sample_1.fastq sample_2.fastq
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33 #end if
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34 -b $maptype.select;
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35 cat SeqSero_result*/Seqsero_result.txt > results.txt;
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36
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37 ]]></command>
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38 <inputs>
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39 <conditional name="jobtype">
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40 <param name="select" type="select" label="Assembly or FASTQ Reads?">
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41 <option value="asm">Genome Assembly</option>
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42 <option value="se">Single-End Reads</option>
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43 <option value="pe">Paired-End Reads</option>
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44 </param>
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1
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45 <when value="asm">
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46 <param name="draft" type="data" format="fasta" label="FASTA" />
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47 </when>
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48 <when value="se">
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49 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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50 </when>
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51 <when value="pe">
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52 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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53 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
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54 </when>
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55 </conditional>
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56
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57 <conditional name="maptype">
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58 <param name="select" type="select" label="Algorithms for BWA mapping?">
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59 <option value="sam">sam</option>
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60 <option value="mem">mem</option>
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61 </param>
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62 </conditional>
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63
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64
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65 </inputs>
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66 <outputs>
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67 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <output name="results" file="results.txt"/>
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75
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76 **Usage: ectyper**
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77
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78 **INPUT**
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79
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80 A fasta assembly
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81
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82 **PERCENTIDENTITY**
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83
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84 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
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85
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86 **PERCENTLENGTH**
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87
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88 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
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89
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90 **verify**
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91
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92 Enable E. Coli. verification
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93
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94 **species**
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95
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96 Enable species identification when non-ecoli genome is found Note: refseq downloading is required when running this option for the first time.
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97
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98 **OUTPUT**
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99 Directory location of output files.
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100 ]]></help>
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101 </tool>
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