Mercurial > repos > yating-l > jbrowsearchivecreator

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
author yating-l
date Thu, 15 Feb 2018 17:05:05 -0500
parents ac83821b0e06
children 43a700afd457
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5:e762f4b9e4bd 6:237707a6b74d
2 This Galaxy tool permits to prepare your files to be ready for JBrowse visualization. 2 This Galaxy tool permits to prepare your files to be ready for JBrowse visualization.
3 3
4 ## Features 4 ## Features
5 1. Similar interface to Hub Archive Creator. 5 1. Similar interface to Hub Archive Creator.
6 2. Convert tracks to GFF3 datatypes (e.g Blastxml => GFF3) in order to import feature data from the flat files 6 2. Convert tracks to GFF3 datatypes (e.g Blastxml => GFF3) in order to import feature data from the flat files
7 3. Generate a zip file including all the tracks and configuration for JBrowse visualization 7 3. Group the tracks
8 4. Group the tracks 8 4. Set the color for each track
9 5. Set the color for each track 9 5. Set the label for each track
10 6. Set the label for each track 10 6. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks!
11 7. Create workflows within Galaxy to automatize pipeline analysis and get them ready to visualization inside JBrowse...in a few clicks!
12 11
13 At the moment, Supported datatypes are: 12 At the moment, Supported datatypes are:
14 - Bam 13 - Bam
15 - Bed 14 - Bed
16 - Splice Junctions (BED 12+1) 15 - Splice Junctions (BED 12+1)
17 - Simple Repeats (BED 4+12) 16 - Simple Repeats (BED 4+12)
18 - BigWig 17 - BigWig
19 - Gff3 18 - Gff3
20 - Gtf 19 - Gtf
21 - Blastxml 20 - Blastxml
21 - BigPsl
22 22
23 ## Installation: 23 ## Installation:
24 1. You would need to add this tool into your Galaxy. 24 1. You would need to add this tool into your Galaxy.
25 1. (strongly preferred) **ToolShed Installation**: Tool is in [testtoolshed](https://testtoolshed.g2.bx.psu.edu/view/yating-l/jbrowse_hub/b7bf45272ab7) 25 1. (strongly preferred) **ToolShed Installation**: Tool is in [testtoolshed](https://testtoolshed.g2.bx.psu.edu/view/yating-l/jbrowse_hub/b7bf45272ab7)
26 2. OR **Local Installation**: See https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial 26 2. OR **Local Installation**: See https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial