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comparison autogenJB2.xml @ 30:8f02a84ee278 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
author fubar
date Wed, 21 Feb 2024 02:57:30 +0000
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29:f728cf0df71d 30:8f02a84ee278
1 <tool id="autogenjb2" name="autogenjb2" version="2.10.0_0" profile="22.05">
2 <description>Files to JBrowse2</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edamInc"/>
7 <xrefs>
8 <xref type="bio.tools">jbrowse2</xref>
9 </xrefs>
10 <expand macro="requirements"/>
11 <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command>
12 <command detect_errors="aggressive"><![CDATA[
13 python '$__tool_directory__/autogenJB2.py'
14 #for $key in $jbrowseme.keys():
15 --collection '$key,$jbrowseme[$key],$jbrowseme[$key].ext'
16 #end for
17 --sessName "Autogen JBrowse"
18 ]]></command>
19 <inputs>
20 <param
21 label="Collection of files specially named to become tracks"
22 name="jbrowseme"
23 type="data_collection">
24 </param>
25 </inputs>
26 <outputs>
27 <data format="html" name="output" label="JBrowse2"/>
28 </outputs>
29
30 <help><![CDATA[
31
32 JBrowse2-in-Galaxy
33 ==================
34
35 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible
36 alternative to JBrowse1-in-Galaxy and Trackster.
37
38 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
39 and detailed track styling is not yet implemented. Send code.
40 JBrowse1 development has now ceased in favour of JBrowse2.
41
42 Use and local viewing
43 =====================
44
45
46 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
47
48 The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history.
49 This can be shared and viewed without Galaxy.
50
51 A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive,
52 assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change
53 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
54
55 With python3 installed,
56
57 *python3 jb2_webserver.py*
58
59 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
60 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
61
62 Overview
63 --------
64
65 JBrowse is a fast, embeddable genome browser built completely with
66 JavaScript and HTML5.
67
68 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
69 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
70 about how to run the command line tools to format your data, and which
71 options need to be supplied and where.
72
73 The JBrowse-in-Galaxy tool has been rejected by `a Galaxy IUC
74 <https://github.com/galaxyproject/tools-iuc/issues>`__, reviewer.
75 It is maintained by https://github.com/fubar2 who you can help you
76 with missing features or bugs in the tool. For the record, he remains unconvinced by the reviewer's logic,
77 and disturbed by the distinctly coercive approach to introducing new code,
78 compared to the more usual method of providing a working PR.
79
80 Options
81 -------
82
83 **Reference or Assembly**
84
85 Choose either a built-in or select one from your history.
86
87 Track coordinates and contig names *must* match this reference precisely
88 or they will not display.
89
90 **Track Groups** represent a set of tracks in a single category.
91
92 Annotation Tracks
93 -----------------
94
95 GFF3/BED
96 ~~~~~~~~
97
98 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
99
100 When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
101 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
102 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
103 well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the
104 lengths of each assembly or reference contig.
105
106 BAM Pileups
107 ~~~~~~~~~~~
108
109 We support BAM files and can automatically generate SNP tracks based on
110 that bam data.
111
112
113 BlastXML
114 ~~~~~~~~
115
116 JiG now supports both blastn and blastp datasets. JiG internally uses a
117 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
118 format amenable to visualization in JBrowse. This tool is also
119 available separately from the IUC on the toolshed.
120
121 **Minimum Gap Size** reflects how long a gap must be before it becomes a
122 real gap in the processed gff3 file. In the picture above, various sizes
123 of gaps can be seen. If the minimum gap size was set much higher, say
124 100nt, many of the smaller gaps would disappear, and the features on
125 both sides would be merged into one, longer feature. This setting is
126 inversely proportional to runtime and output file size. *Do not set this
127 to a low value for large datasets*. By setting this number lower, you
128 will have extremely large outputs and extremely long runtimes. The
129 default was configured based off of the author's experience, but the
130 author only works on small viruses. It is *strongly* recommended that
131 you filter your blast results before display, e.g. picking out the top
132 10 hits or so.
133
134 **Protein blast search** option merely informs underlying tools that
135 they should adjust feature locations by 3x.
136
137
138 @ATTRIBUTION@
139 ]]></help>
140 <expand macro="citations"/>
141 </tool>