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1 <tool id="pangolin" name="PANGOLIN" version="2">
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2 <description>Phylogenetic Assignment of Named Global Outbreak LINeages</description>
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3 <requirements>
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4 <requirement type="package" version="2">pangolin</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Tool exception" />
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8 <exit_code range=":-1" level="fatal" description="Tool exception" />
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9 </stdio>
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10 <version_command>pangolin --version</version_command>
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11 <command>
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12 <![CDATA[
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13 pangolin $query --min-length $minlength --max-ambig $maxambig --threads $threads --alignment
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param name="query" format="fasta" type="data" label="Query fasta file of sequences to analyse" />
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18 <param name="minlength" argument="--min-length" type="integer" value="10000" label="Minimum query length allowed for pangolin to attempt assignment"/>
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19 <param name="maxambig" argument="--max-ambig" type="float" min="0" max="1" value="0.5" label="Maximum proportion of Ns allowed for pangolin to attempt assignment"/>
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20 <param name="threads" argument="--threads" type="integer" value="1" label="Number of threads"/>
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21 </inputs>
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22
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23 <outputs>
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24 <data format="csv" name="lineage" from_work_dir="lineage_report.csv" label="${tool.name} on ${on_string}: lineage" />
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25 <data format="csv" name="alignment" from_work_dir="sequences.aln.fasta" label="${tool.name} on ${on_string}: alignment" />
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26 </outputs>
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27
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28 <tests>
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29 <test>
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30 <param name="query" value="test_consensus.fasta" />
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31 <output name="lineage">
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32 <assert_contents>
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33 <has_text text="C.11" />
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34 <has_text text="passed_qc" />
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35 </assert_contents>
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36 </output>
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37 </test>
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38 </tests>
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39 <help>
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40 **PANGOLIN** stands for "Phylogenetic Assignment of Named Global Outbreak LINeages".
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41
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42 pangolin runs a multinomial logistic regression model trained against lineage assignments based on GISAID data.
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43 </help>
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44 <citations>
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45 <citation type="bibtex">@ARTICLE{andrews_s,
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46 author = {O'Toole, A and McCrone, J and Scher, E},
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47 keywords = {bioinformatics, ngs, coronavirus},
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48 title = {{Phylogenetic Assignment of Named Global Outbreak LINeages}},
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49 url = {https://github.com/cov-lineages/pangolin}
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50 }</citation>
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51 </citations>
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52 </tool>
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