Mercurial > repos > iuc > pangolin
comparison pangolin.xml @ 21:81804a978fc0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 35c4813d132f69036addcc447cc6c4ec7da04d92"
author | iuc |
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date | Sat, 07 May 2022 19:52:10 +0000 |
parents | 14ae456b8cc5 |
children | a2099fb98cdb |
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20:14ae456b8cc5 | 21:81804a978fc0 |
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1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy1" profile="20.01"> | 1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy2" 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@">4.0.5</token> | 4 <token name="@TOOL_VERSION@">4.0.5</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="0.3.17">scorpio</requirement> |
9 <requirement type="package" version="0.23.0">csvtk</requirement> | 9 <requirement type="package" version="0.23.0">csvtk</requirement> |
10 </requirements> | 10 </requirements> |
11 <version_command><![CDATA[pangolin --version]]></version_command> | 11 <version_command><![CDATA[pangolin --version]]></version_command> |
12 <command detect_errors="exit_code"><![CDATA[ | 12 <command detect_errors="exit_code"><![CDATA[ |
13 #if $engine.use_assignment_cache and str($db.source) != "download": | 13 #if $str($engine.analysis_mode) == 'usher' and $engine.use_assignment_cache and str($db.source) != "download": |
14 ## This is no good. Better to fail immediately instead of downloading a lot of data first. | 14 ## This is no good. Better to fail immediately instead of downloading a lot of data first. |
15 echo "Using the latest assignment cache requires downloading the latest version of pangolin-data." 1>&2; exit 1 | 15 echo "Using the latest assignment cache requires downloading the latest version of pangolin-data." 1>&2; exit 1 |
16 #else: | 16 #else: |
17 ## Sanity chceck was ok, lets do the real thing ... | 17 ## Sanity chceck was ok, lets do the real thing ... |
18 #if str($db.source) == "download" | 18 #if str($db.source) == "download" |
20 mkdir datadir && | 20 mkdir datadir && |
21 pangolin --update-data --datadir datadir && | 21 pangolin --update-data --datadir datadir && |
22 #else if str($db.source) == "builtin" | 22 #else if str($db.source) == "builtin" |
23 ln -s $db.db_release.fields.path datadir && | 23 ln -s $db.db_release.fields.path datadir && |
24 #end if | 24 #end if |
25 #if $engine.use_assignment_cache: | 25 #if str($engine.analysis_mode) == 'usher' and $engine.use_assignment_cache: |
26 ## We need to install also the latest UShER assignment cache data. | 26 ## We need to install also the latest UShER assignment cache data. |
27 ## Pangolin has functionality to do so, but uses it incorrectly. | 27 ## Pangolin has functionality to do so, but uses it incorrectly. |
28 ## We use the pangolin function to install into --datadir here, | 28 ## We use the pangolin function to install into --datadir here, |
29 ## then point pangolin to the downloaded file later using | 29 ## then point pangolin to the downloaded file later using |
30 ## its --assignment-cache parameter | 30 ## its --assignment-cache parameter |
215 <has_n_lines n="35" /> | 215 <has_n_lines n="35" /> |
216 <has_n_columns n="16" /> | 216 <has_n_columns n="16" /> |
217 </assert_contents> | 217 </assert_contents> |
218 </output> | 218 </output> |
219 </test> | 219 </test> |
220 <!-- Test that use of latest assignment cache requires downloaded other data --> | |
221 <test expect_failure="true"> | |
222 <param name="input1" value="multiple_alignment.fasta.gz"/> | |
223 <conditional name="engine"> | |
224 <param name="use_assignment_cache" value="true" /> | |
225 </conditional> | |
226 <conditional name="db"> | |
227 <param name="source" value="default" /> | |
228 </conditional> | |
229 </test> | |
220 <!-- test with extra expanded_lineage column --> | 230 <!-- test with extra expanded_lineage column --> |
221 <test expect_num_outputs="1"> | 231 <test expect_num_outputs="1"> |
222 <param name="input1" value="multiple_alignment.fasta.gz"/> | 232 <param name="input1" value="multiple_alignment.fasta.gz"/> |
223 <!-- Test only the default UShER mode for now since the | 233 <!-- Test only the default UShER mode for now since the |
224 pangolearn random forest model uses too much memory | 234 pangolearn random forest model uses too much memory |