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comparison pangolin_2.x.xml @ 0:a12ffc700e29 draft default tip

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"planemo upload"
author iss
date Sun, 11 Apr 2021 07:04:18 +0000
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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>