Mercurial > repos > iuc > pangolin
comparison pangolin.xml @ 29:2f1019071464 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit acc495bd77aa3defdda7ec8d8b84a37d6832f2ee
author | iuc |
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date | Thu, 20 Jul 2023 05:39:41 +0000 |
parents | 9d61d3fa046c |
children | 8ad84c5753ea |
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28:9d61d3fa046c | 29:2f1019071464 |
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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@">4.3</token> | 4 <token name="@TOOL_VERSION@">4.3</token> |
5 <token name="@PANGOLIN_DATA_VERSION@">1.21</token> | 5 <token name="@PANGOLIN_DATA_VERSION@">1.21</token> |
6 <token name="@CONSTELLATIONS_VERSION@">0.1.12</token> | 6 <token name="@CONSTELLATIONS_VERSION@">0.1.12</token> |
10 only compatible versions of that data. --> | 10 only compatible versions of that data. --> |
11 <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@"><![CDATA[^4$|^4\.3$]]></token> | 11 <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@"><![CDATA[^4$|^4\.3$]]></token> |
12 <!-- pangolin-data versions >=1.20 do not contain pangoLEARN models anymore. | 12 <!-- pangolin-data versions >=1.20 do not contain pangoLEARN models anymore. |
13 This version of pangolin still supports pangolearn analysis mode, but only when using | 13 This version of pangolin still supports pangolearn analysis mode, but only when using |
14 older versions of pangolin-data. --> | 14 older versions of pangolin-data. --> |
15 <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT_FOR_PANGOLEARN@">4></token> | 15 <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT_FOR_PANGOLEARN@">4</token> |
16 <!-- a regex describing the scorpio versions that this wrapper version | 16 <!-- a regex describing the scorpio versions that this wrapper version |
17 is backwards-compatible with; can be used with the min_scorpio_version | 17 is backwards-compatible with; can be used with the min_scorpio_version |
18 column of the pangolin_constellations data table to offer only compatible | 18 column of the pangolin_constellations data table to offer only compatible |
19 versions of constellations data. --> | 19 versions of constellations data. --> |
20 <token name="@COMPATIBLE_SCORPIO_DATA_FORMAT@"><![CDATA[(^0\.[1-3]$|^0\.[0-2]\.\d+$|^0\.3\.\d$|^0\.3\.1[0-7]$|^0$)]]></token> | 20 <token name="@COMPATIBLE_SCORPIO_DATA_FORMAT@"><![CDATA[(^0\.[1-3]$|^0\.[0-2]\.\d+$|^0\.3\.\d$|^0\.3\.1[0-7]$|^0$)]]></token> |
32 </xml> | 32 </xml> |
33 </macros> | 33 </macros> |
34 <requirements> | 34 <requirements> |
35 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement> | 35 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement> |
36 <!-- Pin also the versions of all core dependencies - the ones | 36 <!-- Pin also the versions of all core dependencies - the ones |
37 reported with the all-versions option of pangolin plus ucsc-fatovcf, | 37 reported with the all-versions option of pangolin and which have a |
38 which the command is intended to report but currently cannot for | 38 direct impact on the lineage assignment process - to the versions |
39 technical reasons - to the versions you'd get installed in an unpinned | 39 you'd get installed in an unpinned conda install of pangolin at the |
40 conda install of pangolin at the time of release of this wrapper | 40 time of release of this wrapper version! |
41 version! By turning these dependencies into explicit requirements the | 41 By turning these dependencies into explicit requirements the |
42 requirements section of the tool interface becomes the equivalent of | 42 requirements section of the tool interface becomes the equivalent of |
43 the all-versions option as long as the user doesn't update the data | 43 the all-versions option as long as the user doesn't update the data |
44 dependencies. | 44 dependencies. |
45 Wrapper updates are **explicitly encouraged** when new dependency | 45 Wrapper updates are **explicitly encouraged** when new dependency |
46 versions become available. Also, please check for updated dependencies | 46 versions become available. Also, please check for updated dependencies |