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1 <tool id="cpo_tree_galaxy" name="cpoTree" version="0.1.0">
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2 <description>this tool makes tree</description>
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3 <requirements>
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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_tree.py'
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10 '-t $tree'
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11 '-d $distance'
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12 '-m $metadata'
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param type="data" name="tree" format="txt"/>
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17 <param type="data" name="distance" format="tabular" />
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18 <param type="data" name="metadata" format="tabular" />
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19 </inputs>
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20 <outputs>
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21 <data name="tsvSummary" format="png" from_work_dir="tree.png"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="ID" value="BC11-Kpn005_S2"/>
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26 <param name="mlst" value="BC11-Kpn005_S2.mlst"/>
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27 <param name="mobsuitecontig" value="contig_report"/>
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28 <param name="mobsuiteaggregate" value="mobtyper_aggregate_report"/>
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29 <param name="abricate" value="BC11-Kpn005_S2.cp"/>
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30 <param name="rgi" value="BC11-Kpn005_S2.rgi.txt"/>
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31 <param name="plasmidfinder" value="BC11-Kpn005_S2.origins"/>
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32 <param name="expected" value="Klebsiella pneumoniae"/>
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33 <output name="tsvSummary" file="summary.tsv"/>
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34 <output name="txtSummary" file="summary.txt"/>
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35 </test>
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36 </tests>
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37 <help>
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38 This tool parses stuff.
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39 </help>
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40 <citations>
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41 <citation type="bibtex">
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42 @misc{cpo,
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43 author = {j, j},
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44 year = {2018},
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45 title = {cpo_prediction},
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46 publisher = {j},
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47 journal = {j of j},
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48 url = {https://bfjia.net,
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49 }</citation>
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50 </citations>
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51 </tool> |
