Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.xml @ 32:fe48ed5810bd draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
author fubar
date Fri, 23 Feb 2024 07:24:58 +0000
parents 8f02a84ee278
children 15da358c3108
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1 <tool id="autogenjb2" name="autogenjb2" version="2.10.0_0" profile="22.05">
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2 <description>Files to JBrowse2</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edamInc"/>
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7 <xrefs>
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8 <xref type="bio.tools">jbrowse2</xref>
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9 </xrefs>
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10 <expand macro="requirements"/>
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11 <version_command>python '${__tool_directory__}/autogenJB2.py' --version</version_command>
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12 <command detect_errors="aggressive"><![CDATA[
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13 python '$__tool_directory__/autogenJB2.py'
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14 #for $key in $jbrowseme.keys():
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15 --collection '$key,$jbrowseme[$key],$jbrowseme[$key].ext'
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16 #end for
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17 --sessName "Autogen JBrowse"
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18 ]]></command>
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19 <inputs>
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20 <param
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21 label="Collection of files specially named to become tracks"
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22 name="jbrowseme"
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23 type="data_collection">
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24 </param>
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25 </inputs>
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26 <outputs>
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27 <data format="html" name="output" label="JBrowse2"/>
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28 </outputs>
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30 <help><![CDATA[
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32 JBrowse2-in-Galaxy
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33 ==================
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35 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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36 alternative to JBrowse1-in-Galaxy and Trackster.
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37
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38 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
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39 and detailed track styling is not yet implemented. Send code.
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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40 JBrowse1 development has now ceased in favour of JBrowse2.
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41
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42 Use and local viewing
8f02a84ee278 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919
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43 =====================
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46 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
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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.
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49 This can be shared and viewed without Galaxy.
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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,
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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
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53 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
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55 With python3 installed,
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57 *python3 jb2_webserver.py*
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58
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59 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open,
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60 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
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62 Overview
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63 --------
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64
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65 JBrowse is a fast, embeddable genome browser built completely with
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66 JavaScript and HTML5.
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67
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68 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
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69 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
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70 about how to run the command line tools to format your data, and which
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71 options need to be supplied and where.
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72
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73 The JBrowse-in-Galaxy tool has been rejected by `a Galaxy IUC
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74 <https://github.com/galaxyproject/tools-iuc/issues>`__, reviewer.
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75 It is maintained by https://github.com/fubar2 who you can help you
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76 with missing features or bugs in the tool. For the record, he remains unconvinced by the reviewer's logic,
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77 and disturbed by the distinctly coercive approach to introducing new code,
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78 compared to the more usual method of providing a working PR.
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79
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80 Options
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81 -------
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82
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83 **Reference or Assembly**
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84
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85 Choose either a built-in or select one from your history.
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86
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87 Track coordinates and contig names *must* match this reference precisely
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88 or they will not display.
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89
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90 **Track Groups** represent a set of tracks in a single category.
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91
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92 Annotation Tracks
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93 -----------------
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94
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95 GFF3/BED
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96 ~~~~~~~~
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97
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98 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
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99
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100 When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
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101 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
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102 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
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103 well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the
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104 lengths of each assembly or reference contig.
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105
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106 BAM Pileups
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107 ~~~~~~~~~~~
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108
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109 We support BAM files and can automatically generate SNP tracks based on
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110 that bam data.
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111
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112
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113 BlastXML
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114 ~~~~~~~~
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115
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116 JiG now supports both blastn and blastp datasets. JiG internally uses a
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117 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
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118 format amenable to visualization in JBrowse. This tool is also
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119 available separately from the IUC on the toolshed.
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120
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121 **Minimum Gap Size** reflects how long a gap must be before it becomes a
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122 real gap in the processed gff3 file. In the picture above, various sizes
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123 of gaps can be seen. If the minimum gap size was set much higher, say
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124 100nt, many of the smaller gaps would disappear, and the features on
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125 both sides would be merged into one, longer feature. This setting is
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126 inversely proportional to runtime and output file size. *Do not set this
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127 to a low value for large datasets*. By setting this number lower, you
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128 will have extremely large outputs and extremely long runtimes. The
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129 default was configured based off of the author's experience, but the
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130 author only works on small viruses. It is *strongly* recommended that
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131 you filter your blast results before display, e.g. picking out the top
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132 10 hits or so.
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133
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134 **Protein blast search** option merely informs underlying tools that
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135 they should adjust feature locations by 3x.
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136
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137
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138 @ATTRIBUTION@
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139 ]]></help>
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140 <expand macro="citations"/>
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141 </tool>