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comparison autogenJB2.xml @ 19:bde6b1d09f7d draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
author fubar
date Tue, 30 Jan 2024 06:05:03 +0000
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18:2e6c48910819 19:bde6b1d09f7d
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 --outdir '$jbrowseme'
15
16 &&
17
18 cp '$output.files_path/index.html' '$output'
19
20 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
21 #if str($uglyTestingHack) == "enabled":
22 && cp '$trackxml' '$output'
23 #end if
24 ]]></command>
25 <inputs>
26 <param
27 label="Collection of files specially named to become tracks"
28 name="jbrowseme"
29 type="data_collection">
30 </param>
31 <param type="hidden" name="uglyTestingHack" value="" />
32 </inputs>
33 <outputs>
34 <data format="html" name="output" label="JBrowse2 on $reference_genome.genome.element_identifier"/>
35 </outputs>
36
37 <help><![CDATA[
38
39 JBrowse2-in-Galaxy
40 ==================
41
42 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible
43 alternative to JBrowse1-in-Galaxy and Trackster.
44
45 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
46 and detailed track styling is not yet implemented. Send code.
47 JBrowse1 development has now ceased in favour of JBrowse2.
48
49 Use and local viewing
50 =====================
51
52
53 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
54
55 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.
56 This can be shared and viewed without Galaxy.
57
58 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,
59 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
60 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
61
62 With python3 installed,
63
64 *python3 jb2_webserver.py*
65
66 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
67 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
68
69 Overview
70 --------
71
72 JBrowse is a fast, embeddable genome browser built completely with
73 JavaScript and HTML5.
74
75 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
76 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
77 about how to run the command line tools to format your data, and which
78 options need to be supplied and where.
79
80 The JBrowse-in-Galaxy tool has been rejected by `a Galaxy IUC
81 <https://github.com/galaxyproject/tools-iuc/issues>`__, reviewer.
82 It is maintained by https://github.com/fubar2 who you can help you
83 with missing features or bugs in the tool. For the record, he remains unconvinced by the reviewer's logic,
84 and disturbed by the distinctly coercive approach to introducing new code,
85 compared to the more usual method of providing a working PR.
86
87 Options
88 -------
89
90 **Reference or Assembly**
91
92 Choose either a built-in or select one from your history.
93
94 Track coordinates and contig names *must* match this reference precisely
95 or they will not display.
96
97 **Track Groups** represent a set of tracks in a single category.
98
99 Annotation Tracks
100 -----------------
101
102 GFF3/BED
103 ~~~~~~~~
104
105 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
106
107 When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
108 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
109 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
110 well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the
111 lengths of each assembly or reference contig.
112
113 BAM Pileups
114 ~~~~~~~~~~~
115
116 We support BAM files and can automatically generate SNP tracks based on
117 that bam data.
118
119
120 BlastXML
121 ~~~~~~~~
122
123 JiG now supports both blastn and blastp datasets. JiG internally uses a
124 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
125 format amenable to visualization in JBrowse. This tool is also
126 available separately from the IUC on the toolshed.
127
128 **Minimum Gap Size** reflects how long a gap must be before it becomes a
129 real gap in the processed gff3 file. In the picture above, various sizes
130 of gaps can be seen. If the minimum gap size was set much higher, say
131 100nt, many of the smaller gaps would disappear, and the features on
132 both sides would be merged into one, longer feature. This setting is
133 inversely proportional to runtime and output file size. *Do not set this
134 to a low value for large datasets*. By setting this number lower, you
135 will have extremely large outputs and extremely long runtimes. The
136 default was configured based off of the author's experience, but the
137 author only works on small viruses. It is *strongly* recommended that
138 you filter your blast results before display, e.g. picking out the top
139 10 hits or so.
140
141 **Protein blast search** option merely informs underlying tools that
142 they should adjust feature locations by 3x.
143
144
145 @ATTRIBUTION@
146 ]]></help>
147 <expand macro="citations"/>
148 </tool>