annotate jbrowse.xml @ 7:1e74f16adaa1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 942848a0ccd21064ad5d9ee237d1442a5ef47664
author iuc
date Sun, 26 Jun 2016 10:50:15 -0400
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1 <tool id="jbrowse" name="JBrowse" version="0.5.2">
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2 <description>genome browser</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="requirements"/>
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7 <expand macro="stdio"/>
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8 <version_command>python jbrowse.py --version</version_command>
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9 <command><![CDATA[
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11 #if $action.action_select == "create":
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12 mkdir -p $output.files_path;
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13 #else:
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14 cp -R $action.update_jbrowse.extra_files_path $output.files_path;
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15 #end if
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16
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17 ## Copy the XML file into the directory, mostly for debugging
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18 ## but nice if users want to reproduce locally
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19 cp $trackxml $output.files_path/galaxy.xml &&
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20
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21 ## Once that's done, we run the python script to handle the real work
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22 python $__tool_directory__/jbrowse.py
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23
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24 --jbrowse \${JBROWSE_SOURCE_DIR}
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25 #if str($standalone) == "Complete":
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26 --standalone
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27 #end if
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29 --outdir $output.files_path
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30 $trackxml;
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31
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32 #if str($standalone) == "Complete":
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33 mv $output.files_path/index.html $output;
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34 #else:
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35 mv $dummyIndex $output;
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36 #end if
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37
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38
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39 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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40 #if str($uglyTestingHack) == "enabled":
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41 mv $trackxml $output
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42 #end if
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43 ]]></command>
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44 <configfiles>
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45 <configfile name="dummyIndex">
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46 <![CDATA[
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47 <html>
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48 <head>
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49 </head>
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50 <body>
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51 <h1>JBrowse Data Directory</h1>
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52 <p>
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53 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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54 started shipping with the ability to produce just the
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55 "data" directory from a JBrowse instance, rather than a
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56 complete, standalone instance. This was intended to be used
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57 with the in-development Apollo integration, but may have other
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58 uses as well.
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59 </p>
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60 <p>
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61 <u>This is not usable on its own</u>. The output dataset may be
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62 used with Apollo, or may be passed through the "JBrowse -
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63 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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64 JBrowse instance.
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65 </p>
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66 </body>
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67 </html>
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68 ]]>
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69 </configfile>
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70 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
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71 <root>
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72 <metadata>
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73 <gencode>$gencode</gencode>
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74 <genomes>
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75 #if str($action.reference_genome.genome_type_select) == "indexed":
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76 <genome>${action.reference_genome.genomes.fields.path}</genome>
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77 #else
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78 #for $genome in $action.reference_genome.genomes:
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79 <genome>$genome</genome>
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80 #end for
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81 #end if
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82 </genomes>
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83 <general>
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84 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
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85 <trackPadding>${jbgen.trackPadding}</trackPadding>
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86
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87 <shareLink>${jbgen.shareLink}</shareLink>
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88 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
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89 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
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90 <show_nav>${jbgen.show_nav}</show_nav>
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91 <show_overview>${jbgen.show_overview}</show_overview>
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92 <show_menu>${jbgen.show_menu}</show_menu>
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93 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
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94 </general>
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95 </metadata>
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96 <tracks>
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97 #for $tg in $track_groups:
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98 #for $track in $tg.data_tracks:
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99 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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100 <files>
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101 #for $dataset in $track.data_format.annotation:
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102 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />
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103 #end for
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104 </files>
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105
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106 <options>
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107 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast":
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108 <style>
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109 <className>${track.data_format.jbstyle.style_classname}</className>
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110 <description>${track.data_format.jbstyle.style_description}</description>
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111 <label>${track.data_format.jbstyle.style_label}</label>
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112 <height>${track.data_format.jbstyle.style_height}</height>
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113 </style>
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114 <scaling>
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115 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
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116 <method>ignore</method>
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117 <scheme>
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118 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
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119 <color>__auto__</color>
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120 #else
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121 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
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122 #end if
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123 </scheme>
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124 #else
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125 <method>score</method>
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126 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
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127 <scales>
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128 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
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129
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130 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
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131 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
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132 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
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133 #end if
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134 </scales>
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135 <scheme>
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136 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
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137 ## auto_color
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138 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
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139 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
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140 <color>__auto__</color>
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141 #else
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142 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
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143 #end if
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144 #end if
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145 </scheme>
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146 #end if
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147 </scaling>
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148 #end if
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149
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150 #if str($track.data_format.data_format_select) == "wiggle":
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151 <wiggle>
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152 <type>${track.data_format.xyplot}</type>
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153 <variance_band>${track.data_format.var_band}</variance_band>
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154 #if str($track.data_format.scaling.scale_select) == "auto_local":
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155 <autoscale>local</autoscale>
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156 #else if str($track.data_format.scaling.scale_select) == "auto_global":
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157 <autoscale>global</autoscale>
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158 #else:
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159 <min>${track.data_format.scaling.minimum}</min>
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160 <max>${track.data_format.scaling.maximum}</max>
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161 #end if
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162
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163 ## Wiggle tracks need special color config
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164 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
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165 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
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166 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
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167 #else:
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168 <color_pos>__auto__</color_pos>
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169 <color_neg>__auto__</color_neg>
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170 #end if
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171
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172 ## Bicolor pivot config
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173 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
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174 <bicolor_pivot>zero</bicolor_pivot>
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175 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
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176 <bicolor_pivot>mean</bicolor_pivot>
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177 #else:
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178 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
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179 #end if
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180 </wiggle>
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181 #else if str($track.data_format.data_format_select) == "pileup":
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182 <pileup>
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183 <auto_snp>${track.data_format.auto_snp}</auto_snp>
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184 <bam_indices>
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185 #for $dataset in $track.data_format.annotation:
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186 <bam_index>${dataset.metadata.bam_index}</bam_index>
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187 #end for
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188 </bam_indices>
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189 </pileup>
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190 #else if str($track.data_format.data_format_select) == "blast":
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191 <blast>
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192 #if str($track.data_format.blast_parent) != "":
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193 <parent>${track.data_format.blast_parent}</parent>
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194 #end if
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195 <protein>${track.data_format.is_protein}</protein>
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196 <min_gap>${track.data_format.min_gap}</min_gap>
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197 </blast>
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198 #else if str($track.data_format.data_format_select) == "gene_calls":
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199 <gff>
5
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200 <trackType>${track.data_format.track_class}</trackType>
3
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201 #if $track.data_format.match_part.match_part_select:
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202 <match>${track.data_format.match_part.name}</match>
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203 #end if
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204 </gff>
5
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205 ## #else if str($track.data_format.data_format_select) == "sparql":
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206 ## <sparql>
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207 ## <url>${track.data_format.url}</url>
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208 ## <label>${track.data_format.label}</label>
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209 ## <!-- This is going to be an absolutey nightmare -->
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210 ## <query>${track.data_format.query}</query>
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211 ## </sparql>
3
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212 #end if
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213 </options>
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214 </track>
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215 #end for
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216 #end for
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217 </tracks>
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218 </root>
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219 ]]>
1
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220 </configfile>
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221 </configfiles>
0
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222 <inputs>
5
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223 <conditional name="action" label="Action">
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224 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
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225 <option value="create">New JBrowse Instance</option>
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226 <option value="update">Update exising JBrowse Instance</option>
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227 </param>
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228 <when value="create">
6
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229 <expand macro="genome_selector" />
5
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230 </when>
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231 <when value="update">
6
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232 <expand macro="genome_selector"
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233 label="Additional Fasta Sequence(s)"
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234 help="If sequences are selected, they will be added to the existing JBrowse instance. You should not select any sequences if you are simply updating an existing JBrowse instance which already has the required reference sequences."
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235 optional="True"/>
5
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236 <param label="Previous JBrowse Instance"
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237 name="update_jbrowse"
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238 type="data"
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239 format="html" />
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240 </when>
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241 </conditional>
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242
3
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243 <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/>
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244
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245 <param label="Genetic Code" name="gencode" type="select">
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246 <option value="1">1. The Standard Code</option>
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247 <option value="2">2. The Vertebrate Mitochondrial Code</option>
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248 <option value="3">3. The Yeast Mitochondrial Code</option>
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249 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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250 <option value="5">5. The Invertebrate Mitochondrial Code</option>
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251 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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252 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
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253 <option value="10">10. The Euplotid Nuclear Code</option>
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254 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
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255 <option value="12">12. The Alternative Yeast Nuclear Code</option>
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256 <option value="13">13. The Ascidian Mitochondrial Code</option>
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257 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
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258 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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259 <option value="21">21. Trematode Mitochondrial Code</option>
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260 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
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261 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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262 <option value="24">24. Pterobranchia Mitochondrial Code</option>
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263 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
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264 </param>
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265
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266 <repeat name="track_groups" title="Track Group">
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267 <param label="Track Category"
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268 name="category"
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269 type="text"
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270 value="Default"
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271 help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/>
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272 <repeat name="data_tracks" title="Annotation Track">
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273 <conditional name="data_format" label="Track Options">
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274 <param type="select" label="Track Type" name="data_format_select">
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275 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
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276 <option value="pileup">BAM Pileups</option>
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277 <option value="blast">Blast XML</option>
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278 <option value="wiggle">BigWig XY</option>
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279 <option value="vcf">VCF SNPs</option>
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280 <!--<option value="sparql">SPARQL</option>-->
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281 </param>
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282 <when value="blast">
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283 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
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284
3
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285 <param label="Features used in Blast Search"
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286 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."
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287 format="gff3"
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288 name="blast_parent"
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289 optional="true"
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290 type="data"/>
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291
3
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292 <param label="Minimum Gap Size"
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293 help="before a new match_part feature is created"
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294 name="min_gap"
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295 type="integer"
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296 value="10"
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297 min="2" />
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298 <param label="Is this a protein blast search?"
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299 type="boolean"
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300 name="is_protein"
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301 truevalue="true"
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302 falsevalue="false" />
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303
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304 <expand macro="track_styling"
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305 classname="feature"
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306 label="description"
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307 description="Hit_titles"
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308 height="600px"/>
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309 <expand macro="color_selection"
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310 token_scaling_lin_select="false"
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311 token_scaling_log_select="true" />
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312 <expand macro="track_display" />
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313 </when>
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314 <when value="vcf">
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315 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
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316 <expand macro="track_display" />
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317 </when>
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318 <when value="gene_calls">
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319 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
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320 <conditional name="match_part" label="match/match_part data">
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321 <param label="This is match/match_part data"
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322 type="boolean"
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323 name="match_part_select"
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324 truevalue="true"
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325 falsevalue="false" />
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326 <when value="true">
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327 <param label="Match Part Feature Type"
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328 name="name"
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329 type="text"
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330 value="match"
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331 help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here"
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332 optional="False"/>
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333 </when>
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334 <when value="false" />
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335 </conditional>
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336 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
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337 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
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338 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
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339 </param>
3
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340 <expand macro="track_styling" />
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341 <expand macro="color_selection" />
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342 <expand macro="track_display" />
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343 </when>
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344 <when value="pileup">
3
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345 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
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346 <param label="Autogenerate SNP Track"
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347 help="Not recommended for deep coverage BAM files"
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348 type="boolean"
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349 name="auto_snp"
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350 truevalue="true"
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351 falsevalue="false" />
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352 <expand macro="track_display" />
1
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353 </when>
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354 <when value="wiggle">
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355 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
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356
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357 <param label="Use XYPlot"
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358 help="instead of continuous colored band"
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359 type="boolean"
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360 name="xyplot"
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361 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
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362 falsevalue="JBrowse/View/Track/Wiggle/Density" />
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363 <param label="Show variance band"
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364 help="Only for XYPlots"
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365 type="boolean"
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366 name="var_band"
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367 truevalue="true"
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368 falsevalue="false" />
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369
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370 <conditional name="scaling" label="Scaling">
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371 <param type="select" label="Track Scaling" name="scale_select">
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372 <option value="auto_local">Autoscale (local)</option>
3
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373 <option value="auto_global" selected="true">Autoscale (global)</option>
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374 <option value="fixed">Specify Min/Max</option>
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375 </param>
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376 <when value="auto_local"></when>
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377 <when value="auto_global"></when>
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378 <when value="fixed">
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379 <param label="Track minimum" name="minimum"
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380 type="integer" value="0" />
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381 <param label="Track maximum" name="maximum"
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382 type="integer" value="100" />
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383 </when>
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384 </conditional>
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385 <expand macro="color_selection_minmax" />
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386 <expand macro="track_display" />
1
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387 </when>
5
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388 <!--
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389 <when value="sparql">
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390 <param type="text" label="SPARQL Server URL" name="url" />
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391 <param type="text" label="Track Label" name="key" value="SPARQL Genes" />
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diff changeset
392 <param type="text" label="SPARQL Query" name="query" area="true" />
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393 <expand macro="track_display" />
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parents: 3
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394 </when>
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395 -->
1
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parents: 0
diff changeset
396 </conditional>
0
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diff changeset
397 </repeat>
3
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398 </repeat>
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parents: 1
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399
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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400 <expand macro="general_options" />
3
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parents: 1
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401 <param type="hidden" name="uglyTestingHack" value="" />
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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402 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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403 <outputs>
3
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parents: 1
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404 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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405 </outputs>
3
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406 <tests>
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407 <test>
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408 <!-- gencode -->
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409 <param name="genomes" value="merlin.fa"/>
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parents: 1
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410 <param name="gencode" value="1" />
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parents: 1
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411 <param name="standalone" value="Data Directory" />
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iuc
parents: 1
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412 <param name="uglyTestingHack" value="enabled" />
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413 <output name="output" file="gencode/test-1.xml" lines_diff="4" />
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414 </test>
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415 <test>
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416 <param name="genomes" value="merlin.fa"/>
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parents: 1
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417 <param name="gencode" value="11" />
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parents: 1
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418 <param name="standalone" value="Data Directory" />
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iuc
parents: 1
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419 <param name="uglyTestingHack" value="enabled" />
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parents: 1
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420 <output name="output" file="gencode/test.xml" lines_diff="4"/>
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421 </test>
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422 <!--
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423 <test>
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424 <param name="genomes" value="merlin.fa"/>
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iuc
parents: 1
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425 <param name="gencode" value="11" />
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iuc
parents: 1
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426 <param name="standalone" value="Data Directory" />
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iuc
parents: 1
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427 <param name="track_groups_0|category" value="Auto Coloured" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
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428 <param name="track_groups_0|data_tracks_0|data_format" value="gene_calls"/>
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parents: 1
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429 <param name="track_groups_0|data_tracks_0|annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/>
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430 <param name="track_groups_0|data_tracks_0|match_part|match_part_select" value="false"/>
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431 <param name="track_groups_0|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/>
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parents: 1
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432 <param name="track_groups_0|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/>
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parents: 1
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433
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parents: 1
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434
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435 <param name="track_groups_1|category" value="Ignore Scale" />
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iuc
parents: 1
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436 <param name="track_groups_1|data_tracks_0|data_format" value="gene_calls"/>
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437 <param name="track_groups_1|data_tracks_0|annotation" value="gff3/1.gff"/>
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438 <param name="track_groups_1|data_tracks_0|match_part|match_part_select" value="false"/>
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439 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/>
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440 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|color_select" value="manual"/>
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441 <param name="track_groups_1|data_tracks_0|jbcolor_scale|color_score|color|style_color" value="#ff00ff"/>
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442
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443 <param name="track_groups_2|category" value="Scaled Colour" />
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444 <param name="track_groups_2|data_tracks_0|data_format" value="gene_calls"/>
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445 <param name="track_groups_2|data_tracks_0|annotation" value="gff3/1.gff"/>
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446 <param name="track_groups_2|data_tracks_0|match_part|match_part_select" value="false"/>
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447 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="score"/>
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448 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scaling" value="linear"/>
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449 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/>
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450 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/>
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451 <param name="track_groups_2|data_tracks_0|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/>
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452 <param name="track_groups_2|data_tracks_1|data_format" value="gene_calls"/>
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453 <param name="track_groups_2|data_tracks_1|annotation" value="gff3/1.gff"/>
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454 <param name="track_groups_2|data_tracks_1|match_part|match_part_select" value="false"/>
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455 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="score"/>
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456 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scaling" value="linear"/>
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457 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/>
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458 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/>
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459 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/>
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460 <param name="track_groups_2|data_tracks_1|jbcolor_scale|color_score|color_scheme|style_color" value="#0000ff"/>
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461 <param name="track_groups_2|data_tracks_2|data_format" value="gene_calls"/>
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parents: 1
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462 <param name="track_groups_2|data_tracks_2|annotation" value="gff3/1.gff"/>
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463 <param name="track_groups_2|data_tracks_2|match_part|match_part_select" value="false"/>
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parents: 1
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464 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_score_select" value="score"/>
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parents: 1
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465 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scaling" value="linear"/>
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466 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/>
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parents: 1
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467 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|minimum" value="0"/>
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parents: 1
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468 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|score_scales|maximum" value="1000"/>
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parents: 1
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469 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/>
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parents: 1
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470 <param name="track_groups_2|data_tracks_2|jbcolor_scale|color_score|color_scheme|color_select" value="automatic"/>
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parents: 1
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471 <param name="track_groups_2|data_tracks_3|data_format" value="gene_calls"/>
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parents: 1
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472 <param name="track_groups_2|data_tracks_3|annotation" value="gff3/1.gff"/>
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473 <param name="track_groups_2|data_tracks_3|match_part|match_part_select" value="false"/>
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parents: 1
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474 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_score_select" value="score"/>
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iuc
parents: 1
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475 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scaling" value="linear"/>
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parents: 1
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476 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|scale_select" value="automatic"/>
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parents: 1
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477 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|minimum" value="0"/>
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parents: 1
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478 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|score_scales|maximum" value="1000"/>
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parents: 1
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479 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|score_scheme" value="opacity"/>
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480 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|color_select" value="manual"/>
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481 <param name="track_groups_2|data_tracks_3|jbcolor_scale|color_score|color_scheme|style_color" value="#ff0000"/>
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parents: 1
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482
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483 <param name="track_groups_3|category" value="Realistic" />
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484 <param name="track_groups_3|data_tracks_0|data_format" value="gene_calls"/>
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485 <param name="track_groups_3|data_tracks_0|annotation" value="gff3/interpro.gff"/>
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486 <param name="track_groups_3|data_tracks_0|match_part|match_part_select" value="false"/>
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487 <param name="track_groups_3|data_tracks_0|jbcolor_scale|color_score|color_score_select" value="none"/>
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parents: 1
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488 <param name="track_groups_3|data_tracks_0|jbcolor_scale|color|color_select" value="automatic"/>
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489 <param name="track_groups_3|data_tracks_1|data_format" value="gene_calls"/>
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parents: 1
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490 <param name="track_groups_3|data_tracks_1|annotation" value="gff3/2.gff"/>
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491 <param name="track_groups_3|data_tracks_1|match_part|match_part_select" value="true"/>
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492 <param name="track_groups_3|data_tracks_1|match_part|name" value="cDNA_match"/>
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parents: 1
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493 <param name="track_groups_3|data_tracks_1|jbcolor_scale|color_score|color_score_select" value="none"/>
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parents: 1
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494 <param name="track_groups_3|data_tracks_1|jbcolor_scale|color|color_select" value="automatic"/>
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parents: 1
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495
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496 <param name="uglyTestingHack" value="enabled" />
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parents: 1
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497 <output name="output" file="gff3/test.xml" />
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498 </test>
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parents: 1
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499 -->
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parents: 1
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500 </tests>
0
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501 <help><![CDATA[
3
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502 JBrowse-in-Galaxy
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parents: 1
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503 =================
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parents: 1
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504
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505 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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506 alternative to Trackster.
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parents: 1
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507
5
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parents: 3
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508 Overview
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parents: 3
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509 --------
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
510
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
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511 JBrowse is a fast, embeddable genome browser built completely with
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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512 JavaScript and HTML5.
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
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513
3
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parents: 1
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514 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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515 JBrowse installations straight from Galaxy, taking advantage of the
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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516 latest Galaxy features such as dataset collections, sections, and colour
7342f467507b Uploaded v0.4 of JBrowse
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517 pickers. It allows you to build up a JBrowse instance without worrying
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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518 about how to run the command line tools to format your data, and which
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parents: 1
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519 options need to be supplied and where. Additionally it comes with many
7342f467507b Uploaded v0.4 of JBrowse
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520 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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521 nearly impossible to write without the assistance of this tool.
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
522
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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523 The JBrowse-in-Galaxy tool is maintained by `Eric
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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524 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you
7342f467507b Uploaded v0.4 of JBrowse
iuc
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525 encounter missing features or bugs.
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
526
7342f467507b Uploaded v0.4 of JBrowse
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527 Options
7342f467507b Uploaded v0.4 of JBrowse
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528 -------
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
529
7342f467507b Uploaded v0.4 of JBrowse
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530 The first option you encounter is the **Fasta Sequence(s)**. This option
7342f467507b Uploaded v0.4 of JBrowse
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531 now accepts multiple fasta files, allowing you to build JBrowse
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
532 instances that contain data for multiple genomes or chrosomomes
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
533 (generally known as "landmark features" in gff3 terminology.) Up to 30
7342f467507b Uploaded v0.4 of JBrowse
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534 will be shown from the dropdown selector within JBrowse, this is a known
7342f467507b Uploaded v0.4 of JBrowse
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535 issue.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
536
7342f467507b Uploaded v0.4 of JBrowse
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537 **Standalone Instances** are a somewhat in-development feature.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
538 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
539 complete, downloadable file that contains a ready-to-go JBrowse
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
540 instance. This is obviously an anti-feature because users don't want a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
541 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
542 dataset in their history, and admins don't want useless copies of
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
543 JBrowse on disk. Unfortunately we have not come up with the perfect
7342f467507b Uploaded v0.4 of JBrowse
iuc
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544 solution just yet, but we're working on it! In the meantime, users have
7342f467507b Uploaded v0.4 of JBrowse
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545 been given the option to produce just the ``data/`` directory. For those
7342f467507b Uploaded v0.4 of JBrowse
iuc
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546 unfamiliar with JBrowse, the ``data/`` directory contains processed data
7342f467507b Uploaded v0.4 of JBrowse
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547 files, but no way to view them. This feature is additionally implemented
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
548 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
7342f467507b Uploaded v0.4 of JBrowse
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549
7342f467507b Uploaded v0.4 of JBrowse
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550 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
7342f467507b Uploaded v0.4 of JBrowse
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551 which allows users to specify a non standard genetic code, and have
7342f467507b Uploaded v0.4 of JBrowse
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552 JBrowse highlight the correct start and stop codons. If you would like
7342f467507b Uploaded v0.4 of JBrowse
iuc
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553 to use a coding table not provided by this list, please let
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
554 `me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for
7342f467507b Uploaded v0.4 of JBrowse
iuc
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555 this.
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
556
7342f467507b Uploaded v0.4 of JBrowse
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557 **Track Groups** represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse
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558 can be used to let your users understand relationships between large
7342f467507b Uploaded v0.4 of JBrowse
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559 groups of tracks.
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
560
7342f467507b Uploaded v0.4 of JBrowse
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561 .. image:: sections.png
7342f467507b Uploaded v0.4 of JBrowse
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562
7342f467507b Uploaded v0.4 of JBrowse
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563 Annotation Tracks
7342f467507b Uploaded v0.4 of JBrowse
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564 -----------------
7342f467507b Uploaded v0.4 of JBrowse
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565
7342f467507b Uploaded v0.4 of JBrowse
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566 Within Track Groups, you have one or more **Annotation Tracks**. Each
7342f467507b Uploaded v0.4 of JBrowse
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567 Annotation Track is a groups of datasets which have similar styling.
7342f467507b Uploaded v0.4 of JBrowse
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568 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse
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569 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse
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570 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse
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571 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse
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572 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse
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573
7342f467507b Uploaded v0.4 of JBrowse
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574 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse
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575 set of options:
7342f467507b Uploaded v0.4 of JBrowse
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576
7342f467507b Uploaded v0.4 of JBrowse
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577 GFF3/BED/GBK
7342f467507b Uploaded v0.4 of JBrowse
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578 ~~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
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579
7342f467507b Uploaded v0.4 of JBrowse
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580 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse
iuc
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581 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
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582 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse
iuc
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583 data, and have not been tested extensively with other formats. Automatic
7342f467507b Uploaded v0.4 of JBrowse
iuc
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584 min/max detection will likely fail under BED and GBK datasets.
7342f467507b Uploaded v0.4 of JBrowse
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585
7342f467507b Uploaded v0.4 of JBrowse
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586 The data may be of a subclass we call **match/match part** data. This
7342f467507b Uploaded v0.4 of JBrowse
iuc
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587 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse
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588 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse
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589 section on the `GFF3
7342f467507b Uploaded v0.4 of JBrowse
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590 specification <http://www.sequenceontology.org/gff3.shtml>`__ for more
7342f467507b Uploaded v0.4 of JBrowse
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591 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse
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592 the top level match feature name, as it can be one of a few different SO
7342f467507b Uploaded v0.4 of JBrowse
iuc
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593 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse
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594
7342f467507b Uploaded v0.4 of JBrowse
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595 Next up is the **Styling Options** section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse
iuc
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596 properties on how the track is styled. Most of these you will not need
7342f467507b Uploaded v0.4 of JBrowse
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597 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse
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598 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse
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599
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
600 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse
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601
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
602 In the above image you can see some black text, and some blue text. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
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603 source of the black text is configured with the **style.label** option,
7342f467507b Uploaded v0.4 of JBrowse
iuc
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604 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse
iuc
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605 **style.description** option.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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606
7342f467507b Uploaded v0.4 of JBrowse
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607 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse
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608 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
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609
7342f467507b Uploaded v0.4 of JBrowse
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610 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse
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611 files, or using it. If you choose to ignore it, all features will be
7342f467507b Uploaded v0.4 of JBrowse
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612 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse
iuc
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613 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse
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614
7342f467507b Uploaded v0.4 of JBrowse
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615 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse
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616
7342f467507b Uploaded v0.4 of JBrowse
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617 If you choose **Ignore score**, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse
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618 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse
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619 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse
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620 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse
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621 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse
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622 colour palette.
7342f467507b Uploaded v0.4 of JBrowse
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623
7342f467507b Uploaded v0.4 of JBrowse
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624 If you choose **Base on score**, you're faced with a dizzying array of
7342f467507b Uploaded v0.4 of JBrowse
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625 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
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626 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse
iuc
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627 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse
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628
7342f467507b Uploaded v0.4 of JBrowse
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629 The **linear scaling** method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse
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630 directly to a range of output values". **Logarithmic scaling** says
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
631 "please take the log of the score before mapping", and **Blast scaling**
7342f467507b Uploaded v0.4 of JBrowse
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632 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse
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633 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse
iuc
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634 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse
iuc
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635 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse
iuc
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636 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
637
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
638 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse
iuc
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639 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse
iuc
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640 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
641
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
642 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
643 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
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644 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
645 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
646
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
647 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
648 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
649
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
650 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
651 that bam data.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
652
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
653 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
654
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
655 This is *strongly discouraged* for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse
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656 Unfortunately there are no other configuration options exposed for bam
7342f467507b Uploaded v0.4 of JBrowse
iuc
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657 files. If you find JBrowse options you wish to see exposed, please let
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
658 `me <mailto:esr+jig@tamu.edu>`__ know.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
659
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
660 BlastXML
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
661 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
662
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
663 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
664
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
665 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
666 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
667 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
668 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
669
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
670 **Minimum Gap Size** reflects how long a gap must be before it becomes a
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
671 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
672 of gaps can be seen. If the minimum gap size was set much higher, say
7342f467507b Uploaded v0.4 of JBrowse
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673 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
674 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
675 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
676 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
677 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
678 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
679 author only works on small viruses. It is *strongly* recommended that
7342f467507b Uploaded v0.4 of JBrowse
iuc
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680 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
681 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
682
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
683 **Protein blast search** option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
684 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
685
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
686 Styling Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
687 ^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
688
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
689 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
690
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
691 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
692 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
693
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
694 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
695 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
696 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
697
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
698 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
699 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
700
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
701 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
702
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
703 **XYPlot**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
704
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
705 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
706 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
707 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
708 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
709
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
710 **Variance Band** is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
711 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
712 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
713
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
714 **Track Scaling** is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
715 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
716 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
717 the track, and fix the bounds of the viewport to that. E.g. if your
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
718 track ranges from 1-1000, and the region you're currently zoomed to only
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
719 goes from 0-50, then the viewport range will still show 1-1000. This is
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
720 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
721 **autoscaling locally** instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
722 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
723 viewport to re-adjust and show just the 0-50 region. If neither of these
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
724 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
725 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
726
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
727 Colour Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
728 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
729
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
730 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
731 colour.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
732
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
733 As always you may manually choose a colour, or let JiG choose for you.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
734
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
735 One of the more interesting options is the **Bicolor pivot**. This
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
736 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
737 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
738 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
739 tracks.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
740
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
741 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
742 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
743
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
744 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
745
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
746 Known Issues
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
747 ------------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
748
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
749 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
750 selector.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
751 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
752 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
753 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
754
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
755
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
756 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
757 ]]></help>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
758 <citations>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
759 <citation type="doi">10.1101/gr.094607.109</citation>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
760 </citations>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
761 </tool>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
762