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comparison pangolin.xml @ 25:8d6b8f492cb2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
author iuc
date Sun, 15 Jan 2023 10:33:59 +0000
parents 28926e244e85
children bff9c9cce9c0
comparison
equal deleted inserted replaced
24:1714b32064ff 25:8d6b8f492cb2
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@">4.1.2</token> 4 <token name="@TOOL_VERSION@">4.1.3</token>
5 <token name="@PANGOLIN_DATA_VERSION@">1.12</token> 5 <token name="@PANGOLIN_DATA_VERSION@">1.17</token>
6 <token name="@CONSTELLATIONS_VERSION@">0.1.10</token> 6 <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>
7 <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token> 7 <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>
8 <!-- a regex describing the scorpio versions that this wrapper version 8 <!-- a regex describing the scorpio versions that this wrapper version
9 is backwards-compatible with; can be used with the min_scorpio_version 9 is backwards-compatible with; can be used with the min_scorpio_version
10 column of the constellations data table to offer only compatible 10 column of the constellations data table to offer only compatible
71 versions become available. Also, please check for updated dependencies 71 versions become available. Also, please check for updated dependencies
72 when updating the wrapper for other reasons. --> 72 when updating the wrapper for other reasons. -->
73 <requirement type="package" version="0.3.17">scorpio</requirement> 73 <requirement type="package" version="0.3.17">scorpio</requirement>
74 <requirement type="package" version="@PANGOLIN_DATA_VERSION@">pangolin-data</requirement> 74 <requirement type="package" version="@PANGOLIN_DATA_VERSION@">pangolin-data</requirement>
75 <requirement type="package" version="@CONSTELLATIONS_VERSION@">constellations</requirement> 75 <requirement type="package" version="@CONSTELLATIONS_VERSION@">constellations</requirement>
76 <requirement type="package" version="0.5.6">usher</requirement> 76 <requirement type="package" version="0.6.2">usher</requirement>
77 <requirement type="package" version="1.1.0">gofasta</requirement> 77 <requirement type="package" version="1.1.0">gofasta</requirement>
78 <requirement type="package" version="426">ucsc-fatovcf</requirement> 78 <requirement type="package" version="426">ucsc-fatovcf</requirement>
79 <requirement type="package" version="2.24">minimap2</requirement> 79 <requirement type="package" version="2.24">minimap2</requirement>
80 <!-- wrapper-specific requirements to turn pangolin's native 80 <!-- wrapper-specific requirements to turn pangolin's native
81 comma-separated output into tab-separated one and to truncate 81 comma-separated output into tab-separated one and to truncate
82 pangolin's all-versions output. --> 82 pangolin's all-versions output. -->
83 <requirement type="package" version="0.23.0">csvtk</requirement> 83 <requirement type="package" version="0.25.0">csvtk</requirement>
84 <requirement type="package" version="3.4">grep</requirement> 84 <requirement type="package" version="3.4">grep</requirement>
85 </requirements> 85 </requirements>
86 <version_command><![CDATA[pangolin --version]]></version_command> 86 <version_command><![CDATA[pangolin --version]]></version_command>
87 <command detect_errors="exit_code"><![CDATA[ 87 <command detect_errors="exit_code"><![CDATA[
88 ## Prepare a pangolin datadir if required: 88 ## Prepare a pangolin datadir if required:
194 ]]></command> 194 ]]></command>
195 <inputs> 195 <inputs>
196 <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" /> 196 <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" />
197 <conditional name="engine"> 197 <conditional name="engine">
198 <param argument="--analysis-mode" type="select" label="Analysis mode" 198 <param argument="--analysis-mode" type="select" label="Analysis mode"
199 help="The analysis engine to use for lineage assignment. UShER is considered more accurate, but pangoLEARN is faster"> 199 help="The analysis engine to use for lineage assignment. UShER is considered more accurate; pangoLEARN typically requires more memory, but might be faster in some cases.">
200 <option value="usher">UShER</option> 200 <option value="usher">UShER</option>
201 <option value="pangolearn">pangoLEARN</option> 201 <option value="pangolearn">pangoLEARN</option>
202 </param> 202 </param>
203 <when value="usher"> 203 <when value="usher">
204 <expand macro="pangolin_data_sources"> 204 <expand macro="pangolin_data_sources">
260 <data name="align1" format="fasta" label="pangolin alignment on ${on_string}"> 260 <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
261 <filter>alignment</filter> 261 <filter>alignment</filter>
262 </data> 262 </data>
263 </outputs> 263 </outputs>
264 <tests> 264 <tests>
265 <!-- Test only the default UShER mode for now since the
266 pangolearn random forest model uses too much memory
267 see https://github.com/cov-lineages/pangolin/issues/395
265 <test expect_num_outputs="1"> 268 <test expect_num_outputs="1">
266 <param name="input1" value="test1.fasta"/> 269 <param name="input1" value="test1.fasta"/>
267 <conditional name="engine"> 270 <conditional name="engine">
268 <!-- Test only the default UShER mode for now since the
269 pangolearn random forest model uses too much memory
270 see https://github.com/cov-lineages/pangolin/issues/395
271 <param name="analysis_mode" value="pangolearn" /> 271 <param name="analysis_mode" value="pangolearn" />
272 -->
273 <conditional name="pangolin_data"> 272 <conditional name="pangolin_data">
274 <param name="source" value="default" /> 273 <param name="source" value="default" />
275 </conditional> 274 </conditional>
276 </conditional> 275 </conditional>
277 <output name="output1" ftype="tabular"> 276 <output name="output1" ftype="tabular">
280 <has_text text="pass" /> 279 <has_text text="pass" />
281 <has_n_lines n="1" /> 280 <has_n_lines n="1" />
282 </assert_contents> 281 </assert_contents>
283 </output> 282 </output>
284 </test> 283 </test>
284 -->
285 <test expect_num_outputs="1"> 285 <test expect_num_outputs="1">
286 <param name="input1" value="test1.fasta"/> 286 <param name="input1" value="test1.fasta"/>
287 <conditional name="engine"> 287 <conditional name="engine">
288 <conditional name="pangolin_data"> 288 <conditional name="pangolin_data">
289 <param name="source" value="download" /> 289 <param name="source" value="default" />
290 </conditional> 290 </conditional>
291 </conditional> 291 </conditional>
292 <output name="output1" ftype="tabular"> 292 <output name="output1" ftype="tabular">
293 <assert_contents> 293 <assert_contents>
294 <has_text_matching expression="B\.1\.1.*\t\d\.\d\t*PUSHER" /> 294 <has_text_matching expression="B\.1\.1.*\t\d\.\d+\t*PUSHER" />
295 <has_text text="pass" /> 295 <has_text text="pass" />
296 <has_n_lines n="1" /> 296 <has_n_lines n="1" />
297 </assert_contents> 297 </assert_contents>
298 </output> 298 </output>
299 </test> 299 </test>
300 <!-- test download and alignment options -->
300 <test expect_num_outputs="2"> 301 <test expect_num_outputs="2">
301 <param name="input1" value="test1.fasta" /> 302 <param name="input1" value="test1.fasta" />
302 <conditional name="engine"> 303 <conditional name="engine">
303 <!-- Test only the default UShER mode for now since the 304 <!-- Test only the default UShER mode for now since the
304 pangolearn random forest model uses too much memory 305 pangolearn random forest model uses too much memory