Mercurial > repos > iuc > pangolin
comparison pangolin.xml @ 1:f557122d379e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
author | iuc |
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date | Sun, 25 Apr 2021 20:17:07 +0000 |
parents | 0ec813ad2910 |
children | 514a786baaa9 |
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0:0ec813ad2910 | 1:f557122d379e |
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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, |