Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.xml @ 39:bc57164eb270 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit ace841acd53be99494ed9bba8bb9e2ae212d3661
author fubar
date Fri, 01 Mar 2024 01:03:09 +0000
parents 5f39f745682f
children e1a3d3221ed3
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1 <tool id="autogenjb2" name="autogenjb2" version="2.10.2.0" profile="22.05">
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2 <description>Track collection 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 '${__tool_directory__}/autogenJB2.py' --version</version_command>
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12 <command detect_errors="aggressive"><![CDATA[
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13 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 &&
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14 python '$__tool_directory__/autogenJB2.py'
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15 #for $key in $autoCollection.keys():
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16 #if $autoCollection[$key].ext == 'fasta':
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17 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
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18 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
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19 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
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20 #else if $autoCollection[$key].ext in ['bam',]
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21 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index'
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22 #else if $autoCollection[$key].ext in ['cram',]
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23 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index'
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24 #end if
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25 #end for
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26 --outdir '$output.files_path'
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27 --jbrowse2path \${JBROWSE2_PATH}
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28 --sessName "Autogen JBrowse" &&
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30 cp '$output.files_path/index.html' '$output'
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31 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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32 #if str($uglyTestingHack) == "enabled":
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33 && cp '$output.files_path/config.json' '$output'
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34 #end if
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35 ]]></command>
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36 <inputs>
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37 <param
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38 label="Collection of files to become tracks - they must have short, informative names"
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39 name="autoCollection"
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40 type="data_collection">
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41 </param>
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42 <param type="hidden" name="uglyTestingHack" value="" />
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43 </inputs>
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44 <outputs>
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45 <data format="html" name="output" label="AutoJBrowse2"/>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="uglyTestingHack" value="enabled" />
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50 <param name="autoCollection">
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51 <collection type="list">
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52 <element name="Merlin" value="merlin.fa" ftype="fasta"/>
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53 <element name="merlin-sample.bam" value="bam/merlin-sample.bam" ftype="bam"/>
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54 </collection>
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55 </param>
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56 <output name="output">
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57 <assert_contents>
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58 <has_text text='"name": "Merlin",'/>
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59 <has_text text='"name": "merlin-sample.bam",'/>
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60 <has_text text='"uri": "Merlin.fa.gz.fai"'/>
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61 <has_text text='"uri": "bam_0_merlin-sample.bam.bam.bai"'/>
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62
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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69 JBrowse2-in-Galaxy
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70 ==================
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72 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible
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73 alternative to JBrowse1-in-Galaxy and Trackster.
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75 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
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76 and detailed track styling is not yet implemented. Send code.
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77 JBrowse1 development has now ceased in favour of JBrowse2.
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79 Use and local viewing
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80 =====================
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83 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
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85 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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86 This can be shared and viewed without Galaxy.
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87
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88 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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89 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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90 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
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91
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92 With python3 installed,
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93
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94 *python3 jb2_webserver.py*
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95
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96 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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97 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
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98
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99 Overview
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100 --------
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101
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102 JBrowse is a fast, embeddable genome browser built completely with
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103 JavaScript and HTML5.
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104
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105 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
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106 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
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107 about how to run the command line tools to format your data, and which
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108 options need to be supplied and where.
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109
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110 The JBrowse-in-Galaxy tool has been rejected by `a Galaxy IUC
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111 <https://github.com/galaxyproject/tools-iuc/issues>`__, reviewer.
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112 It is maintained by https://github.com/fubar2 who you can help you
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113 with missing features or bugs in the tool. For the record, he remains unconvinced by the reviewer's logic,
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114 and disturbed by the distinctly coercive approach to introducing new code,
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115 compared to the more usual method of providing a working PR.
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116
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117 Options
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118 -------
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119
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120 **Reference or Assembly**
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121
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122 Choose either a built-in or select one from your history.
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123
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124 Track coordinates and contig names *must* match this reference precisely
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125 or they will not display.
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126
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127 **Track Groups** represent a set of tracks in a single category.
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128
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129 Annotation Tracks
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130 -----------------
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131
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132 GFF3/BED
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133 ~~~~~~~~
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134
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135 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
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136
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137 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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138 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
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139 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
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140 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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141 lengths of each assembly or reference contig.
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142
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143 BAM Pileups
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144 ~~~~~~~~~~~
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145
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146 We support BAM files and can automatically generate SNP tracks based on
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147 that bam data.
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148
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149
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150 BlastXML
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151 ~~~~~~~~
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152
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153 JiG now supports both blastn and blastp datasets. JiG internally uses a
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154 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
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155 format amenable to visualization in JBrowse. This tool is also
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156 available separately from the IUC on the toolshed.
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157
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158 **Minimum Gap Size** reflects how long a gap must be before it becomes a
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159 real gap in the processed gff3 file. In the picture above, various sizes
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160 of gaps can be seen. If the minimum gap size was set much higher, say
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161 100nt, many of the smaller gaps would disappear, and the features on
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162 both sides would be merged into one, longer feature. This setting is
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163 inversely proportional to runtime and output file size. *Do not set this
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164 to a low value for large datasets*. By setting this number lower, you
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165 will have extremely large outputs and extremely long runtimes. The
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166 default was configured based off of the author's experience, but the
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167 author only works on small viruses. It is *strongly* recommended that
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168 you filter your blast results before display, e.g. picking out the top
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169 10 hits or so.
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170
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171 **Protein blast search** option merely informs underlying tools that
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172 they should adjust feature locations by 3x.
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173
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174
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175 @ATTRIBUTION@
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176 ]]></help>
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177 <expand macro="citations"/>
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178 </tool>