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comparison pangolin.xml @ 8:cf00be3d99c0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 5a3f70ab430c70b260dd6e0f5b6c53aed2ca5520"
author iuc
date Fri, 13 Aug 2021 19:52:22 +0000
parents 833447821ac9
children c602f4aa863f
comparison
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7:833447821ac9 8:cf00be3d99c0
1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01"> 1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" 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@">3.1.7</token> 4 <token name="@TOOL_VERSION@">3.1.11</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="0.23.0">csvtk</requirement> 8 <requirement type="package" version="0.23.0">csvtk</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 #if str($db.source) == "download" 11 #if str($db.source) == "download"
12 python '$__tool_directory__/fetch_latest_pangolearn.py' --max_retries=$db.max_retries --timeout=$db.timeout && 12 pangolin --update-data --datadir datadir &&
13 #else if str($db.source) == "builtin" 13 #else if str($db.source) == "builtin"
14 ln -s $db.db_release.fields.path datadir && 14 ln -s $db.db_release.fields.path datadir &&
15 #end if 15 #end if
16 pangolin 16 pangolin
17 --threads \${GALAXY_SLOTS:-1} 17 --threads \${GALAXY_SLOTS:-1}
49 <option value="download">Download latest from web</option> 49 <option value="download">Download latest from web</option>
50 <option value="builtin">Use database from Galaxy server</option> 50 <option value="builtin">Use database from Galaxy server</option>
51 <option value="default">Use default database built in to pangolin (not recommended)</option> 51 <option value="default">Use default database built in to pangolin (not recommended)</option>
52 </param> 52 </param>
53 <when value="download"> 53 <when value="download">
54 <param name="max_retries" label="Max download retries" help="How many times to retry downloading the pangoLEARN database" type="integer" value="5" /> 54 <!-- these are currently not supported by the pangolin downloader -->
55 <param name="timeout" label="Download timeout" help="How many seconds to wait when downloading the pangoLEARN database" type="float" value="60.0" /> 55 <!-- <param name="max_retries" label="Max download retries" help="How many times to retry downloading the pangoLEARN database" type="integer" value="5" /> -->
56 <!-- <param name="timeout" label="Download timeout" help="How many seconds to wait when downloading the pangoLEARN database" type="float" value="60.0" /> -->
56 </when> 57 </when>
57 <when value="builtin"> 58 <when value="builtin">
58 <param name="db_release" label="pangoLEARN release" type="select"> 59 <param name="db_release" label="pangoLEARN release" type="select">
59 <options from_data_table="pangolearn"> 60 <options from_data_table="pangolearn">
60 <column name="value" index="0" /> 61 <column name="value" index="0" />
171 <has_text text="USA" /> 172 <has_text text="USA" />
172 <has_n_lines n="35" /> 173 <has_n_lines n="35" />
173 </assert_contents> 174 </assert_contents>
174 </output> 175 </output>
175 </test> 176 </test>
176 <test expect_failure="true">
177 <param name="input1" value="test1.fasta" />
178 <conditional name="db">
179 <param name="source" value="download" />
180 <param name="timeout" value="0.00001" />
181 <param name="max_retries" value="1" />
182 </conditional>
183 <assert_stderr>
184 <has_text text="timed out" />
185 </assert_stderr>
186 </test>
187 </tests> 177 </tests>
188 <help><![CDATA[ 178 <help><![CDATA[
189 179
190 .. class:: infomark 180 .. class:: infomark
191 181
199 model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the 189 model as required. Finally the pangolin tool can use its default built-in model, but this is **not recommended** as the
200 default model rapidly becomes out of date. 190 default model rapidly becomes out of date.
201 191
202 ]]></help> 192 ]]></help>
203 <citations> 193 <citations>
204 <citation type="bibtex"> 194 <citation type="doi">10.1093/ve/veab064</citation>
205 @misc{githubpangolin,
206 author = {O'Toole, Áine},
207 year = {2020},
208 title = {pangolin},
209 publisher = {GitHub},
210 journal = {GitHub repository},
211 url = {https://github.com/cov-lineages/pangolin},
212 }</citation>
213 </citations> 195 </citations>
214 </tool> 196 </tool>