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

"planemo upload"

<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>