annotate jbrowse.xml @ 22:5f70e7fe6077 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author iuc
date Tue, 30 Oct 2018 18:57:53 -0400
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1 <tool id="jbrowse" name="JBrowse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
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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 '${__tool_directory__}/jbrowse.py' --version</version_command>
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9 <command><![CDATA[
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10 #if $action.action_select == "create":
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11 mkdir -p $output.files_path &&
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12 #else:
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13 cp -R $action.update_jbrowse.extra_files_path $output.files_path &&
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14 #end if
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15
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16 ## Copy the XML file into the directory, mostly for debugging
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17 ## but nice if users want to reproduce locally
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18 cp $trackxml $output.files_path/galaxy.xml &&
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19
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20 ## Once that's done, we run the python script to handle the real work
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21 python '$__tool_directory__/jbrowse.py'
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23 --jbrowse \${JBROWSE_SOURCE_DIR}
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24 #if str($standalone) == "Complete":
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25 --standalone
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26 #end if
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28 --outdir $output.files_path
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29 $trackxml &&
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30
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31 #if str($standalone) == "Complete":
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32 mv $output.files_path/index.html $output;
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33 #else:
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34 mv $dummyIndex $output;
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35 #end if
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36
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37 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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38 #if str($uglyTestingHack) == "enabled":
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39 mv $trackxml $output
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40 #end if
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41 ]]></command>
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42 <configfiles>
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43 <configfile name="dummyIndex"><![CDATA[
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44 <html>
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45 <head>
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46 </head>
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47 <body>
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48 <h1>JBrowse Data Directory</h1>
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49 <p>
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50 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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51 started shipping with the ability to produce just the
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52 "data" directory from a JBrowse instance, rather than a
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53 complete, standalone instance. This was intended to be used
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54 with the in-development Apollo integration, but may have other
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55 uses as well.
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56 </p>
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57 <p>
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58 <u>This is not usable on its own</u>. The output dataset may be
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59 used with Apollo, or may be passed through the "JBrowse -
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60 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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61 JBrowse instance.
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62 </p>
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63 </body>
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64 </html>
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65 ]]></configfile>
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66 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
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67 <root>
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68 <metadata>
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69 <gencode>$gencode</gencode>
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70 <genomes>
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71 #if str($reference_genome.genome_type_select) == "indexed":
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72 <genome path="${reference_genome.genomes.fields.path}">
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73 <metadata />
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74 </genome>s
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75 #else
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76 #for $genome in $reference_genome.genomes:
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77 <genome path="$genome">
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78 <metadata>
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79 <dataset id="${__app__.security.encode_id($genome.id)}" hid="${genome.hid}"
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80 size="${genome.get_size(nice_size=True)}"
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81 edam_format="${genome.datatype.edam_format}"
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82 file_ext="${genome.ext}" />
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83 <history id="${__app__.security.encode_id($genome.history_id)}"
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84 user_email="${genome.history.user.email}"
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85 user_id="${genome.history.user_id}"
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86 display_name="${genome.history.get_display_name()}"/>
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87 <metadata
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88 #for (key, value) in $genome.get_metadata().items():
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89 #if "_types" not in $key:
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90 ${key}="${value}"
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91 #end if
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92 #end for
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93 />
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94 <tool
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95 tool_id="${genome.creating_job.tool_id}"
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96 tool_version="${genome.creating_job.tool_version}"
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97 />
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98 </metadata>
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99 </genome>
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100 #end for
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101 #end if
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102 </genomes>
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103 <general>
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104 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
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105 <trackPadding>${jbgen.trackPadding}</trackPadding>
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106
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107 <shareLink>${jbgen.shareLink}</shareLink>
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108 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
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109 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
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110 <show_nav>${jbgen.show_nav}</show_nav>
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111 <show_overview>${jbgen.show_overview}</show_overview>
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112 <show_menu>${jbgen.show_menu}</show_menu>
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113 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
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114 </general>
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115 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl>
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116 </metadata>
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117 <tracks>
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118 #for $tg in $track_groups:
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119 #for $track in $tg.data_tracks:
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120 #if $track.data_format.data_format_select == "rest":
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121 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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122 <url>${track.data_format.url}</url>
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123 </track>
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124 #else:
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125 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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126 <files>
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127 #for $dataset in $track.data_format.annotation:
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128 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}">
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129 <metadata>
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130 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}"
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131 size="${dataset.get_size(nice_size=True)}"
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132 edam_format="${dataset.datatype.edam_format}"
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133 file_ext="${dataset.ext}" />
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134 <history id="${__app__.security.encode_id($dataset.history_id)}"
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135 user_email="${dataset.history.user.email}"
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136 user_id="${dataset.history.user_id}"
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137 display_name="${dataset.history.get_display_name()}"/>
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138 <metadata
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139 #for (key, value) in $dataset.get_metadata().items():
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140 #if "_types" not in $key:
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141 ${key}="${value}"
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142 #end if
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143 #end for
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144 />
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145 <tool
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146 tool_id="${dataset.creating_job.tool_id}"
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147 tool_version="${dataset.creating_job.tool_version}"
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148 />
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149 </metadata>
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150 </trackFile>
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151 #end for
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152 </files>
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153
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154 <options>
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155 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast":
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156 <style>
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157 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins>
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158 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable>
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159 <className>${track.data_format.jbstyle.style_classname}</className>
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160 <description>${track.data_format.jbstyle.style_description}</description>
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161 <label>${track.data_format.jbstyle.style_label}</label>
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162 <height>${track.data_format.jbstyle.style_height}</height>
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163 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight>
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164 </style>
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165 <scaling>
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166 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
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167 <method>ignore</method>
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168 <scheme>
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169 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
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170 <color>__auto__</color>
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171 #else
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172 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
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173 #end if
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174 </scheme>
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175 #else
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176 <method>score</method>
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177 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
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178 <scales>
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179 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
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180
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181 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
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182 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
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183 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
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184 #end if
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185 </scales>
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186 <scheme>
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187 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
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188 ## auto_color
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189 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
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190 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
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191 <color>__auto__</color>
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192 #else
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193 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
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194 #end if
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195 #end if
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196 </scheme>
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197 #end if
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198 </scaling>
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199 <menus>
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200 #for $menu_item in $track.data_format.jbmenu.track_menu:
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201 <menu>
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202 <action>${menu_item.menu_action}</action>
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203 #if str($menu_item.menu_label) != "":
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204 <label>${menu_item.menu_label}</label>
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205 #end if
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206 #if str($menu_item.menu_title) != "":
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207 <title>${menu_item.menu_title}</title>
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208 #end if
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209 #if str($menu_item.menu_url) != "":
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210 <url>${menu_item.menu_url.replace("&", "&amp;").replace("\"", "&quot;")}</url>
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211 #end if
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212 #if str($menu_item.menu_icon) != "":
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213 <iconClass>${menu_item.menu_icon}</iconClass>
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214 #end if
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215 </menu>
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216 #end for
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217 </menus>
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218 #end if
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219
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220 #if str($track.data_format.data_format_select) == "wiggle":
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221 <wiggle>
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222 <type>${track.data_format.xyplot}</type>
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223 <variance_band>${track.data_format.var_band}</variance_band>
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224 #if str($track.data_format.scaling.scale_select) == "auto_local":
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225 <autoscale>local</autoscale>
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226 #else if str($track.data_format.scaling.scale_select) == "auto_global":
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227 <autoscale>global</autoscale>
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228 #else:
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229 <min>${track.data_format.scaling.minimum}</min>
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230 <max>${track.data_format.scaling.maximum}</max>
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231 #end if
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232 <scale>${track.data_format.scale_select2}</scale>
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233
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234 ## Wiggle tracks need special color config
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235 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
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236 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
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237 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
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238 #else:
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239 <color_pos>__auto__</color_pos>
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240 <color_neg>__auto__</color_neg>
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241 #end if
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242
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243 ## Bicolor pivot config
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244 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
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245 <bicolor_pivot>zero</bicolor_pivot>
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246 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
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247 <bicolor_pivot>mean</bicolor_pivot>
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248 #else:
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249 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
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250 #end if
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251 </wiggle>
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252 #else if str($track.data_format.data_format_select) == "pileup":
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253 <pileup>
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254 <auto_snp>${track.data_format.auto_snp}</auto_snp>
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255 <bam_indices>
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256 #for $dataset in $track.data_format.annotation:
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257 <bam_index>${dataset.metadata.bam_index}</bam_index>
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258 #end for
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259 </bam_indices>
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260 </pileup>
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261 #else if str($track.data_format.data_format_select) == "blast":
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262 <blast>
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263 #if str($track.data_format.blast_parent) != "":
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264 <parent>${track.data_format.blast_parent}</parent>
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265 #end if
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266 <protein>${track.data_format.is_protein}</protein>
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267 <min_gap>${track.data_format.min_gap}</min_gap>
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268 <index>${track.data_format.index}</index>
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269 </blast>
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270 #else if str($track.data_format.data_format_select) == "gene_calls":
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271 <gff>
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272 <trackType>${track.data_format.track_config.track_class}</trackType>
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273 #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures':
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274 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
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275 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
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276 #end if
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277 #if str($track.data_format.track_config.canvas_options.subParts) != "":
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278 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
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279 #end if
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280 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
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281 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
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282 #end if
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283 #else if $track.data_format.track_config.track_class == 'JBrowse/View/Track/HTMLFeatures':
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284 #if str($track.data_format.track_config.html_options.transcriptType) != "":
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285 <transcriptType>${track.data_format.track_config.html_options.transcriptType}</transcriptType>
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286 #end if
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287 #end if
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288 #if $track.data_format.match_part.match_part_select:
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289 <match>${track.data_format.match_part.name}</match>
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290 #end if
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291 <index>${track.data_format.index}</index>
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292 </gff>
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293 ## #else if str($track.data_format.data_format_select) == "sparql":
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294 ## <sparql>
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295 ## <url>${track.data_format.url}</url>
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296 ## <label>${track.data_format.label}</label>
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297 ## <!-- This is going to be an absolutey nightmare -->
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298 ## <query>${track.data_format.query}</query>
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299 ## </sparql>
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300 #end if
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301 </options>
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302 </track>
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303 #end if
3
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304 #end for
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305 #end for
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306 </tracks>
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307 <plugins
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308 ComboTrackSelector="${plugins.ComboTrackSelector}"
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309 Bookmarks="${plugins.Bookmarks}"
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310 GCContent="${plugins.GCContent}"
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311 theme="${plugins.theme}"
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312 />
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313 </root>]]></configfile>
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314 </configfiles>
0
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315 <inputs>
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316 <conditional name="reference_genome">
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317 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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318 <option selected="True" value="indexed">Use a built-in genome</option>
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319 <option value="history">Use a genome from history</option>
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320 </param>
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321 <when value="indexed">
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322 <param
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323 help="If your genome of interest is not listed, contact the Galaxy team"
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324 label="Select a reference genome"
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325 name="genomes"
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326 type="select"
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327 >
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328 <options from_data_table="all_fasta">
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329 <filter column="2" type="sort_by" />
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330 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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331 </options>
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332 </param>
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333 </when>
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334 <when value="history">
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335 <param
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336 format="fasta"
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337 label="Select the reference genome"
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338 name="genomes"
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339 type="data"
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340 multiple="True" />
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341 </when>
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342 </conditional>
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343
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344 <param name="standalone" type="boolean" truevalue="Complete" falsevalue="Data Directory" checked="true" label="Produce Standalone Instance" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo"/>
3
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345
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346 <param name="gencode" type="select" label="Genetic Code">
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parents: 1
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347 <option value="1">1. The Standard Code</option>
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parents: 1
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348 <option value="2">2. The Vertebrate Mitochondrial Code</option>
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349 <option value="3">3. The Yeast Mitochondrial Code</option>
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parents: 1
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350 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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parents: 1
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351 <option value="5">5. The Invertebrate Mitochondrial Code</option>
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parents: 1
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352 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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parents: 1
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353 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
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parents: 1
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354 <option value="10">10. The Euplotid Nuclear Code</option>
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parents: 1
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355 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
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parents: 1
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356 <option value="12">12. The Alternative Yeast Nuclear Code</option>
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parents: 1
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357 <option value="13">13. The Ascidian Mitochondrial Code</option>
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parents: 1
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358 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
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parents: 1
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359 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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parents: 1
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360 <option value="21">21. Trematode Mitochondrial Code</option>
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parents: 1
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361 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
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parents: 1
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362 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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parents: 1
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363 <option value="24">24. Pterobranchia Mitochondrial Code</option>
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parents: 1
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364 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
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parents: 1
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365 </param>
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366
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367 <conditional name="action">
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368 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
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369 <option value="create">New JBrowse Instance</option>
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370 <option value="update">Update exising JBrowse Instance</option>
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371 </param>
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372 <when value="create" />
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373 <when value="update">
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374 <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" />
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375 </when>
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376 </conditional>
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377
3
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parents: 1
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378 <repeat name="track_groups" title="Track Group">
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parents: 1
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379 <param label="Track Category"
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parents: 1
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380 name="category"
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parents: 1
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381 type="text"
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382 value="Default"
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383 help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated." optional="False"/>
0
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384 <repeat name="data_tracks" title="Annotation Track">
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385 <conditional name="data_format" label="Track Options">
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386 <param type="select" label="Track Type" name="data_format_select">
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parents: 1
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387 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
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388 <option value="pileup">BAM Pileups</option>
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389 <option value="blast">Blast XML</option>
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390 <option value="wiggle">BigWig XY</option>
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391 <option value="vcf">VCF SNPs</option>
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392 <option value="rest">REST Endpoint</option>
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393 <!--<option value="sparql">SPARQL</option>-->
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394 </param>
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395 <when value="blast">
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396 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
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397
3
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398 <param label="Features used in Blast Search"
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399 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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400 format="gff3"
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parents: 1
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401 name="blast_parent"
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parents: 1
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402 optional="true"
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parents: 1
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403 type="data"/>
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parents: 0
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404
3
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parents: 1
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405 <param label="Minimum Gap Size"
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parents: 1
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406 help="before a new match_part feature is created"
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parents: 1
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407 name="min_gap"
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parents: 1
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408 type="integer"
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parents: 1
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409 value="10"
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parents: 1
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410 min="2" />
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411 <param label="Is this a protein blast search?"
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parents: 1
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412 type="boolean"
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parents: 1
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413 name="is_protein"
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parents: 1
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414 truevalue="true"
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parents: 1
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415 falsevalue="false" />
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416
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417 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
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418
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419 <expand macro="track_styling"
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parents: 1
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420 classname="feature"
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parents: 1
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421 label="description"
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parents: 1
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422 description="Hit_titles"
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parents: 1
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423 height="600px"/>
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parents: 1
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424 <expand macro="color_selection"
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parents: 1
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425 token_scaling_lin_select="false"
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parents: 1
diff changeset
426 token_scaling_log_select="true" />
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parents: 6
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427 <expand macro="track_menu" />
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428 <expand macro="track_display" />
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429 </when>
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430 <when value="vcf">
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parents: 1
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431 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
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432 <expand macro="track_display" />
1
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433 </when>
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434 <when value="gene_calls">
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parents: 1
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435 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
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436 <conditional name="match_part" label="match/match_part data">
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parents: 1
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437 <param label="This is match/match_part data"
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parents: 1
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438 type="boolean"
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parents: 1
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439 name="match_part_select"
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parents: 1
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440 truevalue="true"
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parents: 1
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441 falsevalue="false" />
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parents: 1
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442 <when value="true">
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parents: 1
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443 <param label="Match Part Feature Type"
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parents: 1
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444 name="name"
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parents: 1
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445 type="text"
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446 value="match"
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parents: 19
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447 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. You can leave empty to try autodetection (only works with CanvasFeatures track type)."
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448 optional="True"/>
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parents: 1
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449 </when>
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parents: 1
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450 <when value="false" />
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diff changeset
451 </conditional>
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parents: 6
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452
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parents: 6
diff changeset
453 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
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parents: 6
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454
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parents: 8
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455 <conditional name="track_config">
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456 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
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457 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
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458 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
459 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option>
10
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parents: 8
diff changeset
460 </param>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
461 <when value="JBrowse/View/Track/CanvasFeatures">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
462 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
463 <param label="Transcript type"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
464 name="transcriptType"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
465 type="text"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
466 value=""
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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parents: 8
diff changeset
467 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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parents: 8
diff changeset
468 optional="True"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
469 <param label="Subfeatures type"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
470 name="subParts"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
471 type="text"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
472 value=""
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
473 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
474 optional="True"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
475 <param label="Implied UTRs"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
476 name="impliedUTRs"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
477 type="boolean"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
478 checked="false"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
479 truevalue="true"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
480 falsevalue="false"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
481 help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
482 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
483 </when>
13
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iuc
parents: 12
diff changeset
484 <when value="JBrowse/View/Track/HTMLFeatures">
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
485 <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false">
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
486 <param label="Transcript type"
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
487 name="transcriptType"
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
488 type="text"
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
489 value=""
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
490 help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
491 optional="True"/>
69c5e9c0add0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit bb4fe9cc4bc03918afa525569ed36144a819ce79
iuc
parents: 12
diff changeset
492 </section>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
493 </when>
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
494 <when value="BlastView/View/Track/CanvasFeatures" />
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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parents: 8
diff changeset
495 </conditional>
3
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iuc
parents: 1
diff changeset
496 <expand macro="track_styling" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
497 <expand macro="color_selection" />
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
498 <expand macro="track_menu" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
499 <expand macro="track_display" />
1
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iuc
parents: 0
diff changeset
500 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
501 <when value="pileup">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
502 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
503 <param label="Autogenerate SNP Track"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
504 help="Not recommended for deep coverage BAM files"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
505 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
506 name="auto_snp"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
507 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
508 falsevalue="false" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
509 <expand macro="track_display" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
510 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
511 <when value="wiggle">
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
512 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
513
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
514 <param label="Use XYPlot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
515 help="instead of continuous colored band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
516 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
517 name="xyplot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
518 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
519 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
520 <param label="Show variance band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
521 help="Only for XYPlots"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
522 type="boolean"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
523 name="var_band"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
524 truevalue="true"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
525 falsevalue="false" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
526
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
527 <conditional name="scaling" label="Scaling">
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
528 <param type="select" label="Track Scaling" name="scale_select">
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
529 <option value="auto_local">Autoscale (local)</option>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
530 <option value="auto_global" selected="true">Autoscale (global)</option>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
531 <option value="fixed">Specify Min/Max</option>
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
532 </param>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
533 <when value="auto_local"></when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
534 <when value="auto_global"></when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
535 <when value="fixed">
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
536 <param label="Track minimum" name="minimum"
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
537 type="integer" value="0" />
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
538 <param label="Track maximum" name="maximum"
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
539 type="integer" value="100" />
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
540 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
541 </conditional>
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
542 <param type="select" label="Visual Scaling" name="scale_select2">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
543 <option value="linear" selected="true">Linear</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
544 <option value="log">Logarithmic (Dynamically Calculated)</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
545 </param>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
546 <expand macro="color_selection_minmax" />
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
547 <expand macro="track_display" />
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
548 </when>
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
549 <when value="rest">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
550 <param type="text" label="REST Endpoint" name="url" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
551 </when>
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
552 <!--
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
553 <when value="sparql">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
554 <param type="text" label="SPARQL Server URL" name="url" />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
555 <param type="text" label="Track Label" name="key" value="SPARQL Genes" />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
556 <param type="text" label="SPARQL Query" name="query" area="true" />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
557 <expand macro="track_display" />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
558 </when>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
559 -->
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
560 </conditional>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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parents:
diff changeset
561 </repeat>
3
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parents: 1
diff changeset
562 </repeat>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
563
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
564 <expand macro="general_options" />
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
565 <section name="plugins" title="Plugins" expanded="false">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
566 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
567 label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
568 help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
569 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
570 label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
571 help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
572
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
573 <param
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
574 label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean"
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
575 help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." />
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
576
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
577 <param type="select" label="JBrowse Theme" name="theme">
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
578 <option value="" selected="True">Default</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
579 <option value="Minimalist">Minimalist</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
580 <option value="Dark">Dark</option>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
581 </param>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
582 </section>
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
583
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
584 <param type="hidden" name="uglyTestingHack" value="" />
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
585 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
586 <outputs>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
587 <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
iuc
parents:
diff changeset
588 </outputs>
3
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iuc
parents: 1
diff changeset
589 <tests>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
590 <test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
591 <!-- gencode -->
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
592 <param name="reference_genome|genome_type_select" value="history"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
593 <param name="reference_genome|genomes" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
594 <param name="gencode" value="1" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
595 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
596 <param name="uglyTestingHack" value="enabled" />
19
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iuc
parents: 18
diff changeset
597 <output name="output" file="gencode/test-1.xml" lines_diff="14"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
598 </test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
599 <test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
600 <param name="reference_genome|genome_type_select" value="history"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
601 <param name="reference_genome|genomes" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
602 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
603 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
604 <param name="uglyTestingHack" value="enabled" />
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
605 <output name="output" file="gencode/test.xml" lines_diff="14"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
606 </test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
607 <test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
608 <param name="reference_genome|genome_type_select" value="history"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
609 <param name="reference_genome|genomes" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
610 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
611 <param name="standalone" value="Data Directory" />
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
612 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
613 <param name="category" value="Auto Coloured" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
614 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
615 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
616 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
617 <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
618 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
619 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
620 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
621 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
622 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
623 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
624 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
625 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
626 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
627 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
628 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
629 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
630 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
631 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
632
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
633 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
634 <param name="category" value="Ignore Scale" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
635 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
636 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
637 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
638 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
639 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
640 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
641 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
642 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
643 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
644 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
645 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
646 <param name="color_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
647 <param name="style_color" value="#ff00ff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
648 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
649 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
650 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
651 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 6
diff changeset
652 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
653 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
654
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
655 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
656 <param name="category" value="Scaled Colour" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
657 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
658 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
659 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
660 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
661 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
662 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
663 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
664 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
665 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
666 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
667 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
668 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
669 <param name="scale_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
670 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
671 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
672 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
673 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
674 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
675 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
676 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
677 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
678 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
679 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
680 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
681 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
682 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
683 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
684 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
685 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
686 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
687 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
688 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
689 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
690 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
691 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
692 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
693 <param name="scale_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
694 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
695 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
696 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
697 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
698 <param name="color_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
699 <param name="style_color" value="#0000ff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
700 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
701 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
702 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
703 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
704 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
705 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
706 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
707 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
708 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
709 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
710 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
711 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
712 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
713 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
714 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
715 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
716 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
717 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
718 <param name="scale_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
719 <param name="minimum" value="0"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
720 <param name="maximum" value="1000"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
721 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
722 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
723 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
724 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
725 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
726 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
727 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
728 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
729 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
730 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
731 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
732 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
733 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
734 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
735 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
736 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
737 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
738 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
739 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
740 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
741 <param name="color_score_select" value="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
742 <param name="score_scaling" value="linear"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
743 <conditional name="score_scales">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
744 <param name="scale_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
745 <param name="minimum" value="0"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
746 <param name="maximum" value="1000"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
747 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
748 <conditional name="color_scheme">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
749 <param name="score_scheme" value="opacity"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
750 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
751 <param name="color_select" value="manual"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
752 <param name="style_color" value="#ff0000"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
753 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
754 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
755 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
756 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
757 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
758 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
759 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
760
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
761 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
762 <param name="category" value="Realistic" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
763 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
764 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
765 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
766 <param name="annotation" value="gff3/interpro.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
767 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
768 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
769 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
770 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
771 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
772 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
773 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
774 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
775 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
776 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
777 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
778 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
779 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
780 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
781 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
782 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
783 <param name="annotation" value="gff3/2.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
784 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
785 <param name="match_part_select" value="true"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
786 <param name="name" value="cDNA_match"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
787 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
788 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
789 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
790 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
791 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
792 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
793 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
794 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
795 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
796 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
797 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
798 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
799
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
800 <param name="uglyTestingHack" value="enabled" />
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
801 <output name="output" file="gff3/test.xml" lines_diff="256" />
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
802 </test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
803 <test>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
804 <param name="reference_genome|genome_type_select" value="history"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
805 <param name="reference_genome|genomes" value="merlin.fa"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
806 <param name="gencode" value="11" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
807 <param name="standalone" value="Data Directory" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
808
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
809 <repeat name="track_groups">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
810 <param name="category" value="With menu or index" />
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
811 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
812 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
813 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
814 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
815 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
816 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
817 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
818 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
819 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
820 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
821 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
822 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
823 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
824 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
825 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
826 <section name="jbmenu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
827 <repeat name="track_menu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
828 <param name="menu_action" value="iframeDialog"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
829 <param name="menu_label" value="Some menu item"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
830 <param name="menu_title" value="Frame title"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
831 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
832 <param name="menu_icon" value="dijitIconNewTask"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
833 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
834 <repeat name="track_menu">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
835 <param name="menu_action" value="newWindow"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
836 <param name="menu_label" value="Another menu item"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
837 <param name="menu_title" value="Frame title 2"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
838 <param name="menu_url" value="https://example.com/#!/?id={name}&amp;q={type}&amp;z=&quot;{end}&quot;"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
839 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
840 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
841 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
842 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
843 <repeat name="data_tracks">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
844 <conditional name="data_format">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
845 <param name="data_format_select" value="gene_calls"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
846 <param name="annotation" value="gff3/1.gff"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
847 <param name="index" value="true"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
848 <conditional name="match_part">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
849 <param name="match_part_select" value="false"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
850 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
851 <section name="jbcolor_scale">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
852 <conditional name="color_score">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
853 <param name="color_score_select" value="none"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
854 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
855 <conditional name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
856 <param name="color_select" value="automatic"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
857 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
858 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
859 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
860 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
861 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
862
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
863 <param name="uglyTestingHack" value="enabled" />
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
864 <output name="output" file="menus/test.xml" lines_diff="24"/>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
865 </test>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
866 <test>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
867 <param name="reference_genome|genome_type_select" value="history"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
868 <param name="reference_genome|genomes" value="merlin.fa"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
869 <param name="gencode" value="11" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
870 <param name="standalone" value="Data Directory" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
871
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
872 <repeat name="track_groups">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
873 <param name="category" value="With canvas config" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
874 <repeat name="data_tracks">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
875 <conditional name="data_format">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
876 <param name="data_format_select" value="gene_calls"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
877 <param name="annotation" value="gff3/1.gff"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
878 <conditional name="match_part">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
879 <param name="match_part_select" value="false"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
880 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
881 <conditional name="track_config">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
882 <section name="canvas_options">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
883 <param name="transcriptType" value="transcript"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
884 <param name="subParts" value="exon"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
885 <param name="impliedUTRs" value="true"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
886 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
887 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
888 <section name="jbcolor_scale">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
889 <conditional name="color_score">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
890 <param name="color_score_select" value="none"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
891 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
892 <conditional name="color">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
893 <param name="color_select" value="automatic"/>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
894 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
895 </section>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
896 </conditional>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
897 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
898 </repeat>
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
899
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
900 <param name="uglyTestingHack" value="enabled" />
17
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents: 16
diff changeset
901 <output name="output" file="track_config/test.xml" lines_diff="26"/>
10
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents: 8
diff changeset
902 </test>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
903 <test>
19
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
904 <param name="reference_genome|genome_type_select" value="history"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
905 <param name="reference_genome|genomes" value="merlin.fa"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
906 <param name="gencode" value="11" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
907 <param name="standalone" value="Data Directory" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
908
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
909 <repeat name="track_groups">
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
910 <param name="category" value="Auto Coloured" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
911 <repeat name="data_tracks">
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
912 <conditional name="data_format">
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
913 <param name="data_format_select" value="pileup"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
914 <param name="annotation" value="bam/merlin-sample.bam"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
915 </conditional>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
916 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
917 </repeat>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
918
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
919 <param name="uglyTestingHack" value="enabled" />
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
920 <output name="output" file="bam/test.xml" lines_diff="48"/>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
921 </test>
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
922
8f33c9fbc119 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents: 18
diff changeset
923 <test>
18
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
924 <!-- data_table -->
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
925 <param name="reference_genome|genome_type_select" value="indexed"/>
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
926 <param name="reference_genome|genomes" value="merlin"/>
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
927 <param name="gencode" value="1" />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
928 <param name="standalone" value="Data Directory" />
836d1aa3e89a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents: 17
diff changeset
929 <param name="uglyTestingHack" value="enabled" />
19
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parents: 18
diff changeset
930 <output name="output" file="gencode/test-data_table.xml" lines_diff="6" />
18
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parents: 17
diff changeset
931 </test>
3
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diff changeset
932 </tests>
0
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iuc
parents:
diff changeset
933 <help><![CDATA[
3
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parents: 1
diff changeset
934 JBrowse-in-Galaxy
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iuc
parents: 1
diff changeset
935 =================
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parents: 1
diff changeset
936
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
937 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
938 alternative to Trackster.
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iuc
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diff changeset
939
17
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parents: 16
diff changeset
940 Overview
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff changeset
941 --------
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
942
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
943 JBrowse is a fast, embeddable genome browser built completely with
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
diff changeset
944 JavaScript and HTML5.
ff11d442feed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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parents: 16
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945
3
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iuc
parents: 1
diff changeset
946 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
947 JBrowse installations straight from Galaxy, taking advantage of the
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iuc
parents: 1
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948 latest Galaxy features such as dataset collections, sections, and colour
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parents: 1
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949 pickers. It allows you to build up a JBrowse instance without worrying
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950 about how to run the command line tools to format your data, and which
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951 options need to be supplied and where. Additionally it comes with many
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parents: 1
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952 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse
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953 nearly impossible to write without the assistance of this tool.
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parents: 1
diff changeset
954
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parents: 1
diff changeset
955 The JBrowse-in-Galaxy tool is maintained by `Eric
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parents: 1
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956 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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957 encounter missing features or bugs.
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958
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parents: 1
diff changeset
959 Options
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parents: 1
diff changeset
960 -------
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parents: 1
diff changeset
961
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962 The first option you encounter is the **Fasta Sequence(s)**. This option
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963 now accepts multiple fasta files, allowing you to build JBrowse
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parents: 1
diff changeset
964 instances that contain data for multiple genomes or chrosomomes
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parents: 1
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965 (generally known as "landmark features" in gff3 terminology.) Up to 30
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966 will be shown from the dropdown selector within JBrowse, this is a known
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967 issue.
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parents: 1
diff changeset
968
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969 **Standalone Instances** are a somewhat in-development feature.
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parents: 1
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970 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
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971 complete, downloadable file that contains a ready-to-go JBrowse
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parents: 1
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972 instance. This is obviously an anti-feature because users don't want a
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parents: 1
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973 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse
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974 dataset in their history, and admins don't want useless copies of
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975 JBrowse on disk. Unfortunately we have not come up with the perfect
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976 solution just yet, but we're working on it! In the meantime, users have
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parents: 1
diff changeset
977 been given the option to produce just the ``data/`` directory. For those
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978 unfamiliar with JBrowse, the ``data/`` directory contains processed data
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diff changeset
979 files, but no way to view them. This feature is additionally implemented
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980 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
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diff changeset
981
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diff changeset
982 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
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983 which allows users to specify a non standard genetic code, and have
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984 JBrowse highlight the correct start and stop codons. If you would like
7342f467507b Uploaded v0.4 of JBrowse
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985 to use a coding table not provided by this list, please let
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
986 `me <mailto:esr+jig@tamu.edu>`__ know so that I may add support for
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
987 this.
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diff changeset
988
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diff changeset
989 **Track Groups** represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
990 can be used to let your users understand relationships between large
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
991 groups of tracks.
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parents: 1
diff changeset
992
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parents: 1
diff changeset
993 .. image:: sections.png
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parents: 1
diff changeset
994
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parents: 1
diff changeset
995 Annotation Tracks
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parents: 1
diff changeset
996 -----------------
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parents: 1
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997
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parents: 1
diff changeset
998 Within Track Groups, you have one or more **Annotation Tracks**. Each
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
999 Annotation Track is a groups of datasets which have similar styling.
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parents: 1
diff changeset
1000 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1001 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1002 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1003 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1004 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1005
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1006 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1007 set of options:
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1008
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1009 GFF3/BED/GBK
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1010 ~~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1011
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1012 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1013 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1014 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1015 data, and have not been tested extensively with other formats. Automatic
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1016 min/max detection will likely fail under BED and GBK datasets.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1017
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1018 The data may be of a subclass we call **match/match part** data. This
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1019 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1020 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1021 section on the `GFF3
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents: 6
diff changeset
1022 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more
3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1023 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1024 the top level match feature name, as it can be one of a few different SO
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1025 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1026
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1027 Next up is the **Styling Options** section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1028 properties on how the track is styled. Most of these you will not need
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1029 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1030 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1031
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1032 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1033
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1034 In the above image you can see some black text, and some blue text. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1035 source of the black text is configured with the **style.label** option,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1036 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1037 **style.description** option.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1038
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1039 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1040 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1041
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1042 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1043 files, or using it. If you choose to ignore it, all features will be
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1044 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1045 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1046
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1047 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1048
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1049 If you choose **Ignore score**, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1050 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1051 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1052 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1053 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1054 colour palette.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1055
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1056 If you choose **Base on score**, you're faced with a dizzying array of
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1057 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1058 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1059 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1060
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1061 The **linear scaling** method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1062 directly to a range of output values". **Logarithmic scaling** says
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1063 "please take the log of the score before mapping", and **Blast scaling**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1064 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1065 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1066 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1067 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1068 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1069
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1070 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1071 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1072 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1073
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1074 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1075 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1076 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1077 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1078
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1079 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1080 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1081
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1082 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1083 that bam data.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1084
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1085 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
1086
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1087 This is *strongly discouraged* for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1088 Unfortunately there are no other configuration options exposed for bam
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1089 files. If you find JBrowse options you wish to see exposed, please let
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1090 `me <mailto:esr+jig@tamu.edu>`__ know.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1091
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1092 BlastXML
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1093 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1094
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1095 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1096
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1097 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1098 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1099 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1100 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1101
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1102 **Minimum Gap Size** reflects how long a gap must be before it becomes a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1103 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1104 of gaps can be seen. If the minimum gap size was set much higher, say
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1105 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1106 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1107 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1108 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1109 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1110 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1111 author only works on small viruses. It is *strongly* recommended that
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1112 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1113 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1114
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1115 **Protein blast search** option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1116 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1117
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1118 Styling Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1119 ^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1120
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1121 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1122
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1123 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1124 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1125
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1126 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1127 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1128 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1129
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1130 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1131 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1132
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1133 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1134
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1135 **XYPlot**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1136
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1137 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1138 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1139 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1140 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1141
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1142 **Variance Band** is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1143 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1144 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1145
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1146 **Track Scaling** is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1147 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1148 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1149 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
1150 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
1151 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
1152 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1153 **autoscaling locally** instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1154 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1155 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
1156 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1157 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1158
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1159 Colour Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1160 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1161
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1162 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1163 colour.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1164
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1165 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
1166
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1167 One of the more interesting options is the **Bicolor pivot**. This
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1168 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1169 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1170 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1171 tracks.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1172
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1173 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1174 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1175
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1176 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1177
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1178 Known Issues
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1179 ------------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1180
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1181 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1182 selector.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1183 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1184 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1185 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1186
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1187 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1188 ]]></help>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
1189 <expand macro="citations"/>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1190 </tool>