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comparison pangolin.xml @ 0:b7099144a3c8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
author iuc
date Mon, 12 Apr 2021 20:31:16 +0000
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-1:000000000000 0:b7099144a3c8
1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@" profile="20.01">
2 <description>Phylogenetic Assignment of Outbreak Lineages</description>
3 <macros>
4 <token name="@TOOL_VERSION@">2.3.8</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
8 <requirement type="package" version="0.22.0">csvtk</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 pangolin
12 --threads \${GALAXY_SLOTS:-1}
13 $alignment
14 --outfile report.csv
15 --max-ambig $max_ambig
16 --min-length $min_length
17 '$input1'
18 && csvtk csv2tab report.csv | tail -n-1 >'$output1'
19 #if $alignment
20 && mv sequences.aln.fasta '$align1'
21 #end if
22 ]]></command>
23 <inputs>
24 <param type="data" name="input1" format="fasta" label="Input FASTA File(s)" />
25 <param name="alignment" type="boolean" label="Generate output alignment"
26 truevalue="--alignment" falsevalue="" />
27 <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed"
28 value="0.5" min="0" max="1" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
29 <param argument="--min-length" type="integer" label="Minimum query length allowed"
30 value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
31 </inputs>
32 <outputs>
33 <data name="output1" format="tabular" label="pangolin on ${on_string}">
34 <actions>
35 <action name="column_names" type="metadata" default="taxon,lineage,probability,pangoLEARN_version,status,note" />
36 </actions>
37 </data>
38 <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
39 <filter>alignment</filter>
40 </data>
41 </outputs>
42 <tests>
43 <test expect_num_outputs="1">
44 <param name="input1" value="test1.fasta"/>
45 <output name="output1" file="result1.tsv" ftype="tabular" />
46 </test>
47 <test expect_num_outputs="2">
48 <param name="alignment" value="--alignment" />
49 <param name="input1" value="test1.fasta" />
50 <output name="output1" file="result1.tsv" ftype="tabular" />
51 <output name="align1" file="aln1.fasta" ftype="fasta" />
52 </test>
53 </tests>
54 <help><![CDATA[
55
56 .. class:: infomark
57
58 `Pangolin <https://cov-lineages.org/pangolin.html>`_ (Phylogenetic Assignment of Named Global Outbreak LINeages)
59 is used to assign a SARS-CoV-2 genome sequence the most likely lineage based on the PANGO nomenclature system.
60
61 ]]></help>
62 <citations>
63 <citation type="bibtex">
64 @misc{githubpangolin,
65 author = {O'Toole, Áine},
66 year = {2020},
67 title = {pangolin},
68 publisher = {GitHub},
69 journal = {GitHub repository},
70 url = {https://github.com/cov-lineages/pangolin},
71 }</citation>
72 </citations>
73 </tool>