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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 </requirements>
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6
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7 <command>kleborate -a `echo $input | tr ',' ' '` $r $kaptive_k $kaptive_o -o $output </command>
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8
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9 <inputs>
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10 <param format="fasta" name="input" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/>
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11
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12 <param name="r" type="select" label="Turn on resistance genes screening (default: no resistance gene screening):">
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13 <option value="">no</option>
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14 <option value="-r">yes</option>
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15 </param>
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16
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17 <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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18 <option value="">no</option>
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19 <option value="--kaptive_k">yes</option>
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20 </param>
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21
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22 <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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23 <option value="">no</option>
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24 <option value="--kaptive_o">yes</option>
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25 </param>
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26
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27 </inputs>
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28
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29 <outputs>
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30 <data format="tabular" name="output" />
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31 </outputs>
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32
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33 <tests>
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34 <test>
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35 <param name="input" value="KP011_S63.scfd.fasta " />
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36 <param name="input" value="KP012_S64.scfd.fasta " />
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37 <param name="r" value="-r"/>
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38 <param name="kaptive_k" value="--kaptive_k"/>
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39 <param name="kaptive_o" value=""/>
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40 <output name="output" file="Kleborate_results.txt" />
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41 </test>
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42 </tests>
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43
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44 <help>
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45 For full documentation, please go to the Kleborate wiki (https://github.com/katholt/Kleborate/wiki)
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46 </help>
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47 <citations>
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48 <citation type="doi">10.1101/2020.12.14.422303</citation>
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49 </citations>
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50 </tool>
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51
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52
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53
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