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1 <tool id="kleboratetool" name="Kleborate" version="0.1.0">
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2 <description>Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae</description>
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3 <requirements>
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4 <requirement type="package" version="2.0.4">kleborate</requirement>
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5 <requirement type="package" version="0.5.1">kaptive</requirement>
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6 <requirement type="package" version="2.10.1">blast</requirement>
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7 </requirements>
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8
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9 <command>kleborate -a `echo $input | tr ',' ' '` $r $kaptive_k $kaptive_o -o $output </command>
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10
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11 <inputs>
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12 <param format="fasta" name="input" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/>
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13
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14 <param name="r" type="select" label="Turn on resistance genes screening (default: no resistance gene screening):">
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15 <option value="">no</option>
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16 <option value="-r">yes</option>
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17 </param>
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18
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19 <param name="kaptive_k" type="select" label="Turn on Kaptive screening of K loci (default: do not run Kaptive for K loci):">
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20 <option value="">no</option>
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21 <option value="--kaptive_k">yes</option>
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22 </param>
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23
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24 <param name="kaptive_o" type="select" label="Turn on Kaptive screening of O loci (default: do not run Kaptive for O loci):">
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25 <option value="">no</option>
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26 <option value="--kaptive_o">yes</option>
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27 </param>
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28
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29 </inputs>
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30
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31 <outputs>
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32 <data format="tabular" name="output" />
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33 </outputs>
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34
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35 <tests>
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36 <test>
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37 <param name="input" value="KP011_S63.scfd.fasta " />
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38 <param name="input" value="KP012_S64.scfd.fasta " />
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39 <param name="r" value="-r"/>
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40 <param name="kaptive_k" value="--kaptive_k"/>
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41 <param name="kaptive_o" value=""/>
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42 <output name="output" file="Kleborate_results.txt" />
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43 </test>
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44 </tests>
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45
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46 <help>
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47 For full documentation, please go to the Kleborate wiki (https://github.com/katholt/Kleborate/wiki)
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48 </help>
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49 <citations>
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50 <citation type="doi">10.1101/2020.12.14.422303</citation>
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51 </citations>
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52 </tool>
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53
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54
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55
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