Mercurial > repos > iss > pangolin
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pangolin_2.x.xml Sun Apr 11 07:04:18 2021 +0000 @@ -0,0 +1,52 @@ +<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>