Mercurial > repos > fubar > jbrowse2
comparison autogenJB2.xml @ 40:e1a3d3221ed3 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 92901862ebe87a9c12f026608a34fbee347c4c78
author | fubar |
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date | Fri, 01 Mar 2024 02:22:44 +0000 |
parents | bc57164eb270 |
children | 4181e97c70a7 |
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39:bc57164eb270 | 40:e1a3d3221ed3 |
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64 </output> | 64 </output> |
65 </test> | 65 </test> |
66 </tests> | 66 </tests> |
67 <help><![CDATA[ | 67 <help><![CDATA[ |
68 | 68 |
69 JBrowse2-in-Galaxy | 69 Autogenerated JBrowse2 |
70 ================== | 70 ====================== |
71 | 71 |
72 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible | 72 Given a collection of datatypes suited for making JB2 tracks, this tool will create a working JBrowse2 configuration. |
73 alternative to JBrowse1-in-Galaxy and Trackster. | 73 A paf track requires a nested collection with the paf file and all the genomes used in creating it. |
74 | 74 |
75 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes, | |
76 and detailed track styling is not yet implemented. Send code. | |
77 JBrowse1 development has now ceased in favour of JBrowse2. | |
78 | 75 |
79 Use and local viewing | 76 Use and local viewing |
80 ===================== | 77 ===================== |
81 | 78 |
82 | 79 |
107 about how to run the command line tools to format your data, and which | 104 about how to run the command line tools to format your data, and which |
108 options need to be supplied and where. | 105 options need to be supplied and where. |
109 | 106 |
110 The JBrowse-in-Galaxy tool has been rejected by `a Galaxy IUC | 107 The JBrowse-in-Galaxy tool has been rejected by `a Galaxy IUC |
111 <https://github.com/galaxyproject/tools-iuc/issues>`__, reviewer. | 108 <https://github.com/galaxyproject/tools-iuc/issues>`__, reviewer. |
112 It is maintained by https://github.com/fubar2 who you can help you | |
113 with missing features or bugs in the tool. For the record, he remains unconvinced by the reviewer's logic, | |
114 and disturbed by the distinctly coercive approach to introducing new code, | |
115 compared to the more usual method of providing a working PR. | |
116 | 109 |
117 Options | 110 Options |
118 ------- | 111 ------- |
119 | 112 |
120 **Reference or Assembly** | 113 **Reference or Assembly** |