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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 891eca7a697643c9b5365781bbab5b655972ffdc
author yating-l
date Mon, 25 Jun 2018 16:05:01 -0400
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1 # JBrowse Hub Creator
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2 This Galaxy tool is used to prepare your files to be ready for JBrowse visualization.
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4 ## Features
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5 1. Similar interface to Hub Archive Creator.
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6 2. Convert tracks to GFF3 datatypes (e.g Blastxml => GFF3) in order to import feature data from the flat files
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7 3. Group the tracks
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8 4. Set the color for each track
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9 5. Set the label for each track
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10 6. Support generating Tabix Indexed CanVasFeatures tracks
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11 7. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks!
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13 At the moment, Supported datatypes are:
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14 - BAM
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15 - BED
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16 - Generic BED
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17 - Splice Junctions (BED 12+1)
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18 - Simple Repeats (BED 4+12)
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19 - BLAT alignment (BigPsl)
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20 - BLAST alignment (BED 12+12)
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21 - BigWig
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22 - GFF3
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23 - GTF
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24 - Blast XML output
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26 ## Installation:
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28 **ToolShed Installation**:
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30 - The JBrowse Archive Creator tool is published at [ToolShed Repository](https://toolshed.g2.bx.psu.edu/view/yating-l/jbrowsearchivecreator)
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32 - Refer to [Installing Tools into Galaxy](https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial) tutorial if you want to learn how to install a tool from ToolShed.
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34 ## Future
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35 See [TODO.md](todo.md) for more information
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37 ## Contribute
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39 - Source Code: https://github.com/goeckslab/jbrowse-archive-creator.git
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41 ## Support
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43 If you are having issues, please let us know.
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45 - For more information about how to use G-OnRamp:
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46 - [Wilson Leung](wleung@wustl.edu) - Product owner and developer
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47 - [Yating Liu](yliu41@wustl.edu) - Community manager and developer
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49 - For more information about the project vision, or for partneship:
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50 - [Elgin, Sarah](selgin@wustl.edu) - PI
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51 - [Jeremy Goecks](jgoecks@gwu.edu) - PI
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53 ## License
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55 The project is licensed under the Academic Free License 3.0. See [LICENSE.txt](LICENSE.txt).