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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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14
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15 ln -s $fasta1 sample_1.fastq;
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16 ln -s $fastq2 sample_2.fastq;
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17
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18 $__tool_directory__/ectyper.py
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19 -i ecoliA.fasta for a single file
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20 -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna for multiple files
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21 -i ecoli_folder for a folder
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22 -i ecoli_folder for a folder
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23 -d PERCENTIDENTITY
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24 -l PERCENTLENGTH
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25 -o OUTPUT;
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26 cat SeqSero_result*/Seqsero_result.txt > results.txt;
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27
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28 ]]></command>
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29 <inputs>
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30 <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
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31 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" />
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32 <param name="numofthr" type="select" label="Number of threads">
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33 <option value="1">1</option>
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34 <option value="2">2</option>
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35 <option value="3">3</option>
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36 <option value="4">4</option>
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37 </param>
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38 <param name="maptype" type="select" label="Algorithms for BWA mapping?">
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39 <option value="mem">mem</option>
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40 <option value="sam">sam</option>
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41 </param>
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42
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43
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44 </inputs>
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45 <outputs>
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46 <data format="txt" label="ectyper Results" name="results" from_work_dir="results.txt"/>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <output name="results" file="results.txt"/>
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51 </test>
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52 </tests>
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53 <help><![CDATA[
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54
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55 **Usage: ectyper**
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56
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57 **INPUT**
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58
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59 Location of new file(s). Can be a single file or a directory
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60
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61 **PERCENTIDENTITY**
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62
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63 Percentage of identity wanted to use against the database. From 0 to 100, default is 90%.
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64
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65 **PERCENTLENGTH**
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66
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67 Percentage of length wanted to use against the database. From 0 to 100, default is 50%.
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68
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69 **verify**
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70
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71 Enable E. Coli. verification
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72
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73 **species**
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74
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75 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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76
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77 **OUTPUT**
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78 Directory location of output files.
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79 ]]></help>
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80 </tool>
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