Mercurial > repos > iss > pangolin
view 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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<tool id="pangolin" name="PANGOLIN" version="2"> <description>Phylogenetic Assignment of Named Global Outbreak LINeages</description> <requirements> <requirement type="package" version="2">pangolin</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> <exit_code range=":-1" level="fatal" description="Tool exception" /> </stdio> <version_command>pangolin --version</version_command> <command> <![CDATA[ pangolin $query --min-length $minlength --max-ambig $maxambig --threads $threads --alignment ]]> </command> <inputs> <param name="query" format="fasta" type="data" label="Query fasta file of sequences to analyse" /> <param name="minlength" argument="--min-length" type="integer" value="10000" label="Minimum query length allowed for pangolin to attempt assignment"/> <param name="maxambig" argument="--max-ambig" type="float" min="0" max="1" value="0.5" label="Maximum proportion of Ns allowed for pangolin to attempt assignment"/> <param name="threads" argument="--threads" type="integer" value="1" label="Number of threads"/> </inputs> <outputs> <data format="csv" name="lineage" from_work_dir="lineage_report.csv" label="${tool.name} on ${on_string}: lineage" /> <data format="csv" name="alignment" from_work_dir="sequences.aln.fasta" label="${tool.name} on ${on_string}: alignment" /> </outputs> <tests> <test> <param name="query" value="test_consensus.fasta" /> <output name="lineage"> <assert_contents> <has_text text="C.11" /> <has_text text="passed_qc" /> </assert_contents> </output> </test> </tests> <help> **PANGOLIN** stands for "Phylogenetic Assignment of Named Global Outbreak LINeages". pangolin runs a multinomial logistic regression model trained against lineage assignments based on GISAID data. </help> <citations> <citation type="bibtex">@ARTICLE{andrews_s, author = {O'Toole, A and McCrone, J and Scher, E}, keywords = {bioinformatics, ngs, coronavirus}, title = {{Phylogenetic Assignment of Named Global Outbreak LINeages}}, url = {https://github.com/cov-lineages/pangolin} }</citation> </citations> </tool>