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1 <tool id="ectyper" name="ectyper" version="0.1">
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2 <requirements>
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3 <requirement type="package" version="0.1">ectyper</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 #if $jobtype.select == "asm"
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7 ln -s $jobtype.draft sample.fasta;
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8 #else if $jobtype.select == "se"
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9 ln -s $jobtype.fastq1 sample_1.fastq;
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10 #else if $jobtype.select == "pe"
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11 ln -s $jobtype.fastq1 sample_1.fastq;
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12 ln -s $jobtype.fastq2 sample_2.fastq;
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13 #end if
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14
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15 $__tool_directory__/ectyper
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16 #if $jobtype.select == "asm"
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17 -i sample.fasta
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18 #else if $jobtype.select == "se"
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19 -i sample_1.fastq
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20 #else if $jobtype.select == "pe"
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21 -i sample_1.fastq sample_2.fastq
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22 #end if
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23 -d $percent_identity
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24 -l $percent_length
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25 -o "./"; cat ./output/output.csv > results.csv;
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26
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27 ]]></command>
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28 <inputs>
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29 <conditional name="jobtype">
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30 <param name="select" type="select" label="Assembly or FASTQ Reads?">
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31 <option value="asm">Genome Assembly</option>
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32 <option value="se">Single-End Reads</option>
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33 <option value="pe">Paired-End Reads</option>
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34 </param>
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35 <when value="asm">
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36 <param name="draft" type="data" format="fasta" label="FASTA" />
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37 </when>
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38 <when value="se">
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39 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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40 </when>
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41 <when value="pe">
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42 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
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43 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
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44 </when>
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45 </conditional>
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46
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47 <param name="percent_identity" type="integer" label="Percent identity required for an allele match [default 90]" value="90" />
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48 <param name="percent_length" type="integer" label="Percent length required for an allele match [default 50]" value="50" />
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49
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50 </inputs>
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51 <outputs>
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52 <data format="csv" label="ectyper Results" name="${input.name}.ectperResults" from_work_dir="*.csv"/>
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53 </outputs>
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54
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55 <help><![CDATA[
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56
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57 **Usage: ectyper**
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58
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59 **INPUT**
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60
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61 A fasta assembly or single or paired end reads
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62
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63 **PERCENTIDENTITY**
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64
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65 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
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66
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67 **PERCENTLENGTH**
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68
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69 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
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70
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71 https://github.com/phac-nml/ecoli_serotyping
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72
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73 ]]></help>
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74 </tool>
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