Mercurial > repos > fubar > jbrowse2

annotate autogenJB2.xml @ 36:5f39f745682f draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 80b849766a962bac4bd0bb8cb69c118cc42699cd-dirty
author fubar
date Thu, 29 Feb 2024 00:47:58 +0000
parents 15da358c3108
children bc57164eb270
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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 '${__tool_directory__}/autogenJB2.py' --version</version_command>
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12 <command detect_errors="aggressive"><![CDATA[
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13 python '$__tool_directory__/autogenJB2.py'
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14 #for $key in $autoCollection.keys():
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15 #if $autoCollection[$key].ext == 'fasta':
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16 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
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17 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf']
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18 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key'
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19 #else if $autoCollection[$key].ext in ['bam',]
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20 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index'
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21 #else if $autoCollection[$key].ext in ['cram',]
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22 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index'
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23 #end if
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24 #end for
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25 --outdir '$output.files_path'
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26 --sessName "Autogen JBrowse" &&
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28 cp '$output.files_path/index.html' '$output'
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29 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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30 #if str($uglyTestingHack) == "enabled":
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31 && cp '$output.files_path/config.json' '$output'
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32 #end if
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33 ]]></command>
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34 <inputs>
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35 <param
35
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36 label="Collection of files to become tracks - they must have short, informative names"
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37 name="autoCollection"
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38 type="data_collection">
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39 </param>
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40 <param type="hidden" name="uglyTestingHack" value="" />
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41 </inputs>
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42 <outputs>
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43 <data format="html" name="output" label="AutoJBrowse2"/>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="uglyTestingHack" value="enabled" />
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48 <param name="autoCollection">
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49 <collection type="list">
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50 <element name="Merlin" value="merlin.fa" ftype="fasta"/>
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51 <element name="merlin-sample.bam" value="bam/merlin-sample.bam" ftype="bam"/>
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52 </collection>
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53 </param>
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54 <output name="output">
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55 <assert_contents>
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56 <has_text text='"name": "Merlin",'/>
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57 <has_text text='"name": "merlin-sample.bam",'/>
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58 <has_text text='"uri": "Merlin.fa.gz.fai"'/>
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59 <has_text text='"uri": "bam_0_merlin-sample.bam.bam.bai"'/>
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60
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61 </assert_contents>
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62 </output>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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67 JBrowse2-in-Galaxy
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68 ==================
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70 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible
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71 alternative to JBrowse1-in-Galaxy and Trackster.
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73 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes,
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74 and detailed track styling is not yet implemented. Send code.
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75 JBrowse1 development has now ceased in favour of JBrowse2.
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77 Use and local viewing
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78 =====================
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81 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
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83 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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84 This can be shared and viewed without Galaxy.
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86 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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87 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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88 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py*
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89
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90 With python3 installed,
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91
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92 *python3 jb2_webserver.py*
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93
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94 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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95 but the script appears to be running, try pointing your web browser to the default of *localhost:8080*
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96
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97 Overview
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98 --------
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99
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100 JBrowse is a fast, embeddable genome browser built completely with
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101 JavaScript and HTML5.
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102
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103 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
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104 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying
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105 about how to run the command line tools to format your data, and which
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106 options need to be supplied and where.
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107
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108 The JBrowse-in-Galaxy tool has been rejected by `a Galaxy IUC
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109 <https://github.com/galaxyproject/tools-iuc/issues>`__, reviewer.
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110 It is maintained by https://github.com/fubar2 who you can help you
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111 with missing features or bugs in the tool. For the record, he remains unconvinced by the reviewer's logic,
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112 and disturbed by the distinctly coercive approach to introducing new code,
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113 compared to the more usual method of providing a working PR.
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114
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115 Options
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116 -------
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117
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118 **Reference or Assembly**
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119
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120 Choose either a built-in or select one from your history.
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121
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122 Track coordinates and contig names *must* match this reference precisely
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123 or they will not display.
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124
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125 **Track Groups** represent a set of tracks in a single category.
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126
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127 Annotation Tracks
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128 -----------------
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129
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130 GFF3/BED
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131 ~~~~~~~~
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132
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133 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region.
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134
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135 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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136 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
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137 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
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138 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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139 lengths of each assembly or reference contig.
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140
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141 BAM Pileups
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142 ~~~~~~~~~~~
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143
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144 We support BAM files and can automatically generate SNP tracks based on
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145 that bam data.
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146
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147
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148 BlastXML
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149 ~~~~~~~~
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150
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151 JiG now supports both blastn and blastp datasets. JiG internally uses a
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152 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
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153 format amenable to visualization in JBrowse. This tool is also
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154 available separately from the IUC on the toolshed.
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155
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156 **Minimum Gap Size** reflects how long a gap must be before it becomes a
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157 real gap in the processed gff3 file. In the picture above, various sizes
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158 of gaps can be seen. If the minimum gap size was set much higher, say
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159 100nt, many of the smaller gaps would disappear, and the features on
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160 both sides would be merged into one, longer feature. This setting is
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161 inversely proportional to runtime and output file size. *Do not set this
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162 to a low value for large datasets*. By setting this number lower, you
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163 will have extremely large outputs and extremely long runtimes. The
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164 default was configured based off of the author's experience, but the
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165 author only works on small viruses. It is *strongly* recommended that
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166 you filter your blast results before display, e.g. picking out the top
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167 10 hits or so.
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168
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169 **Protein blast search** option merely informs underlying tools that
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170 they should adjust feature locations by 3x.
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171
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172
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173 @ATTRIBUTION@
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174 ]]></help>
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175 <expand macro="citations"/>
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176 </tool>