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comparison pangolin.xml @ 15:f8a93c0fe44d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"
author iuc
date Wed, 15 Dec 2021 19:39:17 +0000
parents 1db21543b8ff
children 8fb2cb7de889
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14:1db21543b8ff 15:f8a93c0fe44d
1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01"> 1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01">
2 <description>Phylogenetic Assignment of Outbreak Lineages</description> 2 <description>Phylogenetic Assignment of Outbreak Lineages</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">3.1.17</token> 4 <token name="@TOOL_VERSION@">3.1.17</token>
5 </macros> 5 </macros>
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="0.3.16">scorpio</requirement>
8 <requirement type="package" version="0.23.0">csvtk</requirement> 9 <requirement type="package" version="0.23.0">csvtk</requirement>
9 </requirements> 10 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
11 #if str($db.source) == "download" 12 #if str($db.source) == "download"
12 pangolin --update-data --datadir datadir && 13 pangolin --update-data --datadir datadir &&
43 <param argument="--min-length" type="integer" label="Minimum query length allowed" 44 <param argument="--min-length" type="integer" label="Minimum query length allowed"
44 value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/> 45 value="10000" min="0" help="Minimum query length allowed for pangolin to attempt assignment"/>
45 <param name="include_header" type="boolean" label="Include header line in output file" 46 <param name="include_header" type="boolean" label="Include header line in output file"
46 truevalue="true" falsevalue="false" /> 47 truevalue="true" falsevalue="false" />
47 <conditional name="db"> 48 <conditional name="db">
48 <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database"> 49 <param type="select" name="source" label="pangoLEARN source" help="Where to find the pangoLEARN database. While 'Download latest from web' is recommended, if errors occur see the warning in the main help text below.">
49 <option value="download">Download latest from web</option> 50 <option value="download">Download latest from web</option>
50 <option value="builtin">Use database from Galaxy server</option> 51 <option value="builtin">Use database from Galaxy server</option>
51 <option value="default">Use default database built in to pangolin (not recommended)</option> 52 <option value="default">Use default database built in to pangolin (not recommended)</option>
52 </param> 53 </param>
53 <when value="download"> 54 <when value="download">
160 assignment, and the default option for this tool is to download the latest version of the model before the pangolin 161 assignment, and the default option for this tool is to download the latest version of the model before the pangolin
161 tool runs. A pangoLEARN data manager exists so that the Galaxy admin can download specific versions of the pangoLEARN 162 tool runs. A pangoLEARN data manager exists so that the Galaxy admin can download specific versions of the pangoLEARN
162 model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the 163 model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the
163 default model rapidly becomes out of date. 164 default model rapidly becomes out of date.
164 165
166 .. class:: warningmark
167
168 The "Download latest from web" updates the pangolin database but not the pangolin (and scorpio) software. If
169 the database format changes this can cause the pangolin job and the tool to fail. The solution to this kind of
170 failure is to update the pangolin tool installed in the Galaxy server.
165 ]]></help> 171 ]]></help>
166 <citations> 172 <citations>
167 <citation type="doi">10.1093/ve/veab064</citation> 173 <citation type="doi">10.1093/ve/veab064</citation>
168 </citations> 174 </citations>
169 </tool> 175 </tool>