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5
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1 <tool id="cpo_prediction_parser" name="cpo_prediction_parser" version="0.1.0">
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2 <description>This tool combines outputs from MLST, ResFinder, PlasmidFinder, Mobsuite, RGI into a TSV for the cpo_prediction workflow</description>
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3 <requirements>
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1
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4 <requirement type="package" version="0.23.4">pandas</requirement>
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5 <requirement type="package" version="3.6">python</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 python '$__tool_directory__/cpo_galaxy_prediction.py'
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12
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10 '-i $contig.element_identifier'
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1
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11 '-m $mlst'
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12 '-c $mobsuitecontig'
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13 '-f $mobsuiteaggregate'
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18
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14 '-a $resfinder'
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1
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15 '-r $rgi'
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16 '-e $expected'
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17 '-s $__tool_directory__/scheme_species_map.tab'
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18 '-p $plasmidfinder'
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18
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19 '-d $mash'
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1
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20 ]]>
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21 </command>
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22 <inputs>
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12
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23 <param type="data" name="contig"/>
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1
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24 <param type="data" name="mlst" format="tabular" />
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25 <param type="data" name="mobsuitecontig" format="tabular" />
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26 <param type="data" name="mobsuiteaggregate" format="tabular" />
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18
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27 <param type="data" name="resfinder" format="tabular" />
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1
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28 <param type="data" name="rgi" format="tabular" />
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29 <param type="data" name="plasmidfinder" format="tabular" />
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18
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30 <param type="data" name="mash" format ="tabular"/>
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13
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31 <param type="text" name="expected" optional ="false"/>
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1
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32 </inputs>
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33 <outputs>
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34 <data name="tsvSummary" format="tabular" from_work_dir="summary.tsv"/>
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18
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35 <data name="tsvSummaryExistingFormat" format="tabular" from_work_dir="summary.linda.tsv"/>
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36 <data name="txtSummary" format="txt" from_work_dir="summary.txt"/>
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1
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37 </outputs>
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38 <tests>
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39 <test>
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40 <param name="ID" value="BC11-Kpn005_S2"/>
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41 <param name="mlst" value="BC11-Kpn005_S2.mlst"/>
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42 <param name="mobsuitecontig" value="contig_report"/>
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43 <param name="mobsuiteaggregate" value="mobtyper_aggregate_report"/>
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44 <param name="abricate" value="BC11-Kpn005_S2.cp"/>
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45 <param name="rgi" value="BC11-Kpn005_S2.rgi.txt"/>
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46 <param name="plasmidfinder" value="BC11-Kpn005_S2.origins"/>
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47 <param name="expected" value="Klebsiella pneumoniae"/>
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48 <output name="tsvSummary" file="summary.tsv"/>
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6
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49 <output name="tsvSummary" file="summary.txt"/>
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1
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50 </test>
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51 </tests>
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52 <help>
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53 This tool parses stuff.
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54 </help>
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55 <citations>
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56 <citation type="bibtex">
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57 @misc{cpo,
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58 author = {j, j},
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59 year = {2018},
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60 title = {cpo_prediction},
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61 publisher = {j},
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62 journal = {j of j},
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63 url = {https://bfjia.net,
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64 }</citation>
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65 </citations>
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66 </tool> |
