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comparison pangolin.xml @ 1:de3ceb419d91 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
author iuc
date Sun, 25 Apr 2021 20:16:28 +0000
parents b7099144a3c8
children 68e94cfc9e6d
comparison
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0:b7099144a3c8 1:de3ceb419d91
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
8 <requirement type="package" version="0.22.0">csvtk</requirement> 8 <requirement type="package" version="0.22.0">csvtk</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #if str($db.source) == "download"
12 python '$__tool_directory__/fetch_latest_pangolearn.py' &&
13 #else if str($db.source) == "builtin"
14 ln -s $db.db_release.fields.path datadir &&
15 #end if
11 pangolin 16 pangolin
12 --threads \${GALAXY_SLOTS:-1} 17 --threads \${GALAXY_SLOTS:-1}
18 #if str($db.source) == "download" or str($db.source) == "builtin"
19 --datadir 'datadir'
20 #end if
13 $alignment 21 $alignment
14 --outfile report.csv 22 --outfile report.csv
15 --max-ambig $max_ambig 23 --max-ambig $max_ambig
16 --min-length $min_length 24 --min-length $min_length
17 '$input1' 25 '$input1'
26 truevalue="--alignment" falsevalue="" /> 34 truevalue="--alignment" falsevalue="" />
27 <param argument="--max-ambig" type="float" label="Maximum proportion of Ns allowed" 35 <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" /> 36 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" 37 <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"/> 38 value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
39 <conditional name="db">
40 <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database">
41 <option value="download">Download latest from web</option>
42 <option value="builtin">Use database from Galaxy server</option>
43 <option value="default">Use default database built in to pangolin (not recommended)</option>
44 </param>
45 <when value="download">
46 </when>
47 <when value="builtin">
48 <param name="db_release" label="pangoLEARN release" type="select">
49 <options from_data_table="pangolearn">
50 <column name="value" index="0" />
51 <column name="name" index="1" />
52 <column name="path" index="3" />
53 <filter type="sort_by" column="0"/>
54 </options>
55 </param>
56 </when>
57 <when value="default">
58 </when>
59 </conditional>
31 </inputs> 60 </inputs>
32 <outputs> 61 <outputs>
33 <data name="output1" format="tabular" label="pangolin on ${on_string}"> 62 <data name="output1" format="tabular" label="pangolin on ${on_string}">
34 <actions> 63 <actions>
35 <action name="column_names" type="metadata" default="taxon,lineage,probability,pangoLEARN_version,status,note" /> 64 <action name="column_names" type="metadata" default="taxon,lineage,probability,pangoLEARN_version,status,note" />
40 </data> 69 </data>
41 </outputs> 70 </outputs>
42 <tests> 71 <tests>
43 <test expect_num_outputs="1"> 72 <test expect_num_outputs="1">
44 <param name="input1" value="test1.fasta"/> 73 <param name="input1" value="test1.fasta"/>
45 <output name="output1" file="result1.tsv" ftype="tabular" /> 74 <conditional name="db">
75 <param name="source" value="download" />
76 </conditional>
77 <output name="output1">
78 <assert_contents>
79 <has_text text="B.1.1" />
80 <has_text text="passed_qc" />
81 </assert_contents>
82 </output>
46 </test> 83 </test>
47 <test expect_num_outputs="2"> 84 <test expect_num_outputs="2">
48 <param name="alignment" value="--alignment" /> 85 <param name="alignment" value="--alignment" />
49 <param name="input1" value="test1.fasta" /> 86 <param name="input1" value="test1.fasta" />
50 <output name="output1" file="result1.tsv" ftype="tabular" /> 87 <conditional name="db">
88 <param name="source" value="download" />
89 </conditional>
90 <output name="output1">
91 <assert_contents>
92 <has_text text="B.1.1" />
93 <has_text text="passed_qc" />
94 </assert_contents>
95 </output>
51 <output name="align1" file="aln1.fasta" ftype="fasta" /> 96 <output name="align1" file="aln1.fasta" ftype="fasta" />
52 </test> 97 </test>
98 <test expect_num_outputs="1">
99 <param name="input1" value="test1.fasta"/>
100 <conditional name="db">
101 <param name="source" value="builtin" />
102 </conditional>
103 <output name="output1">
104 <assert_contents>
105 <has_text text="2021-04-21" />
106 </assert_contents>
107 </output>
108 </test>
53 </tests> 109 </tests>
54 <help><![CDATA[ 110 <help><![CDATA[
55 111
56 .. class:: infomark 112 .. class:: infomark
57 113
58 `Pangolin <https://cov-lineages.org/pangolin.html>`_ (Phylogenetic Assignment of Named Global Outbreak LINeages) 114 `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. 115 is used to assign a SARS-CoV-2 genome sequence the most likely lineage based on the PANGO nomenclature system.
116
117 Pangolin uses the `pangoLEARN <https://github.com/cov-lineages/pangoLEARN>`_ stored model for lineage assignment. This
118 model is updated more frequently than the pangolin tool is. In general one should use the most recent model for lineage
119 assignment, and the default option for this tool is to download the latest version of the model before the pangolin
120 tool runs. A pangoLEARN data manager exists so that the Galaxy admin can download specific versions of the pangoLEARN
121 model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the
122 default model rapidly becomes out of date.
60 123
61 ]]></help> 124 ]]></help>
62 <citations> 125 <citations>
63 <citation type="bibtex"> 126 <citation type="bibtex">
64 @misc{githubpangolin, 127 @misc{githubpangolin,