Mercurial > repos > iss > pangolin
comparison pangolin_2.x.xml @ 0:a12ffc700e29 draft default tip
"planemo upload"
author | iss |
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date | Sun, 11 Apr 2021 07:04:18 +0000 |
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-1:000000000000 | 0:a12ffc700e29 |
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1 <tool id="pangolin" name="PANGOLIN" version="2"> | |
2 <description>Phylogenetic Assignment of Named Global Outbreak LINeages</description> | |
3 <requirements> | |
4 <requirement type="package" version="2">pangolin</requirement> | |
5 </requirements> | |
6 <stdio> | |
7 <exit_code range="1:" level="fatal" description="Tool exception" /> | |
8 <exit_code range=":-1" level="fatal" description="Tool exception" /> | |
9 </stdio> | |
10 <version_command>pangolin --version</version_command> | |
11 <command> | |
12 <![CDATA[ | |
13 pangolin $query --min-length $minlength --max-ambig $maxambig --threads $threads --alignment | |
14 ]]> | |
15 </command> | |
16 <inputs> | |
17 <param name="query" format="fasta" type="data" label="Query fasta file of sequences to analyse" /> | |
18 <param name="minlength" argument="--min-length" type="integer" value="10000" label="Minimum query length allowed for pangolin to attempt assignment"/> | |
19 <param name="maxambig" argument="--max-ambig" type="float" min="0" max="1" value="0.5" label="Maximum proportion of Ns allowed for pangolin to attempt assignment"/> | |
20 <param name="threads" argument="--threads" type="integer" value="1" label="Number of threads"/> | |
21 </inputs> | |
22 | |
23 <outputs> | |
24 <data format="csv" name="lineage" from_work_dir="lineage_report.csv" label="${tool.name} on ${on_string}: lineage" /> | |
25 <data format="csv" name="alignment" from_work_dir="sequences.aln.fasta" label="${tool.name} on ${on_string}: alignment" /> | |
26 </outputs> | |
27 | |
28 <tests> | |
29 <test> | |
30 <param name="query" value="test_consensus.fasta" /> | |
31 <output name="lineage"> | |
32 <assert_contents> | |
33 <has_text text="C.11" /> | |
34 <has_text text="passed_qc" /> | |
35 </assert_contents> | |
36 </output> | |
37 </test> | |
38 </tests> | |
39 <help> | |
40 **PANGOLIN** stands for "Phylogenetic Assignment of Named Global Outbreak LINeages". | |
41 | |
42 pangolin runs a multinomial logistic regression model trained against lineage assignments based on GISAID data. | |
43 </help> | |
44 <citations> | |
45 <citation type="bibtex">@ARTICLE{andrews_s, | |
46 author = {O'Toole, A and McCrone, J and Scher, E}, | |
47 keywords = {bioinformatics, ngs, coronavirus}, | |
48 title = {{Phylogenetic Assignment of Named Global Outbreak LINeages}}, | |
49 url = {https://github.com/cov-lineages/pangolin} | |
50 }</citation> | |
51 </citations> | |
52 </tool> |