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1 <tool id="kleboratetool" name="Kleborate" version="0.1.0">
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2 <description> 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="2.1.0">kleborate</requirement>
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5 <requirement type="package" version="2.0.0">kaptive</requirement>
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6 </requirements>
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7
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8 <!-- kleborateold -a `echo $input | tr ',' ' '` $r $kaptive_k $kaptive_o -o $output
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9 /home/linuxipg/Kleborate/kleborate-runner.py -->
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10 <command detect_errors="aggressive"><![CDATA[
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11 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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12 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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13 #set $named_input_files = ''
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14 #for $input_file in $input_files
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15 ## Add single quotes around each input file identifier
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16 #set $_input_file = "'{}'".format($input_file.element_identifier)
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17 ln -s '${input_file}' ${_input_file} &&
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18 #set $named_input_files = $named_input_files + ' ' + $_input_file
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19 #end for
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20
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21 kleborate $r $kaptive_k $kaptive_o -o $output --min_identity $ident --min_coverage $cov -a $named_input_files
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22 ]]></command>
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23
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24 <inputs>
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25 <param format="fasta" name="input_files" type="data" label="Genome fasta file : " multiple="true" display="checkboxes"/>
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26
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27 <param name="r" type="select" label="Turn on resistance genes screening (default: no resistance gene screening):">
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28 <option value="">no</option>
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29 <option value="-r">yes</option>
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30 </param>
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31
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32 <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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33 <option value="">no</option>
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34 <option value="--kaptive_k">yes</option>
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35 </param>
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36
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37 <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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38 <option value="">no</option>
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39 <option value="--kaptive_o">yes</option>
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40 </param>
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41
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42 <param name="ident" type="text" area="false" value="90.0" label="Minimum alignment percent identity for main results:"/>
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43 <param name="cov" type="text" area="false" value="80.0" label="Minimum alignment percent coverage for main results:"/>
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44
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45 </inputs>
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46
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47 <outputs>
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48 <data format="tabular" name="output" />
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49 </outputs>
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50
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51 <tests>
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52 <test>
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53 <param name="input" value="KP011_S63.scfd.fasta " />
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54 <param name="input" value="KP012_S64.scfd.fasta " />
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55 <param name="r" value="-r"/>
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56 <param name="kaptive_k" value="--kaptive_k"/>
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57 <param name="kaptive_o" value=""/>
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58 <output name="output" file="Kleborate_results.txt" />
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59 </test>
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60 </tests>
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61
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62 <help>
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63 For full documentation, please go to the Kleborate wiki (https://github.com/katholt/Kleborate/wiki)
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64 </help>
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65 <citations>
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66 <citation type="doi">10.1101/2020.12.14.422303</citation>
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67 <citation type="doi">10.1038/s41467-021-24448-3</citation>
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68 <citation type="doi">10.1099/mgen.0.000102</citation>
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69 </citations>
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70 </tool>
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