annotate jbrowse.xml @ 11:4cbceec1d6b4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 172014e3f03ea00dfd5fcd689e1246d001e82288
author iuc
date Wed, 14 Dec 2016 09:19:48 -0500
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1 <tool id="jbrowse" name="JBrowse" 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 <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 $output;
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35 #end if
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36
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37
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38 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph.
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39 #if str($uglyTestingHack) == "enabled":
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40 mv $trackxml $output
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41 #end if
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42 ]]></command>
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43 <configfiles>
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44 <configfile name="dummyIndex">
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45 <![CDATA[
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46 <html>
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47 <head>
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48 </head>
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49 <body>
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50 <h1>JBrowse Data Directory</h1>
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51 <p>
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52 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?)
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53 started shipping with the ability to produce just the
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54 "data" directory from a JBrowse instance, rather than a
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55 complete, standalone instance. This was intended to be used
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56 with the in-development Apollo integration, but may have other
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57 uses as well.
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58 </p>
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59 <p>
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60 <u>This is not usable on its own</u>. The output dataset may be
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61 used with Apollo, or may be passed through the "JBrowse -
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62 Convert to Standalone" tool in Galaxy to "upgrade" to a full
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63 JBrowse instance.
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64 </p>
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65 </body>
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66 </html>
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67 ]]>
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68 </configfile>
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69 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
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70 <root>
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71 <metadata>
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72 <gencode>$gencode</gencode>
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73 <genomes>
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74 #if str($reference_genome.genome_type_select) == "indexed":
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75 <genome>${reference_genome.genomes.fields.path}</genome>
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76 #else
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77 #for $genome in $reference_genome.genomes:
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78 <genome>$genome</genome>
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79 #end for
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80 #end if
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81 </genomes>
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82 <general>
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83 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
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84 <trackPadding>${jbgen.trackPadding}</trackPadding>
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86 <shareLink>${jbgen.shareLink}</shareLink>
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87 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
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88 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
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89 <show_nav>${jbgen.show_nav}</show_nav>
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90 <show_overview>${jbgen.show_overview}</show_overview>
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91 <show_menu>${jbgen.show_menu}</show_menu>
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92 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
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93 </general>
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94 </metadata>
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95 <tracks>
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96 #for $tg in $track_groups:
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97 #for $track in $tg.data_tracks:
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98 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
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99 <files>
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100 #for $dataset in $track.data_format.annotation:
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101 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />
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102 #end for
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103 </files>
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104
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105 <options>
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106 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast":
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107 <style>
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108 <className>${track.data_format.jbstyle.style_classname}</className>
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109 <description>${track.data_format.jbstyle.style_description}</description>
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110 <label>${track.data_format.jbstyle.style_label}</label>
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111 <height>${track.data_format.jbstyle.style_height}</height>
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112 </style>
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113 <scaling>
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114 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
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115 <method>ignore</method>
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116 <scheme>
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117 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
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118 <color>__auto__</color>
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119 #else
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120 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
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121 #end if
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122 </scheme>
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123 #else
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124 <method>score</method>
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125 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
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126 <scales>
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127 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
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128
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129 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
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130 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
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131 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
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132 #end if
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133 </scales>
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134 <scheme>
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135 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
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136 ## auto_color
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137 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
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138 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
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139 <color>__auto__</color>
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140 #else
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141 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
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142 #end if
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143 #end if
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144 </scheme>
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145 #end if
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146 </scaling>
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147 <menus>
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148 #for $menu_item in $track.data_format.jbmenu.track_menu:
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149 <menu>
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150 <action>${menu_item.menu_action}</action>
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151 #if str($menu_item.menu_label) != "":
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152 <label>${menu_item.menu_label}</label>
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153 #end if
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154 #if str($menu_item.menu_title) != "":
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155 <title>${menu_item.menu_title}</title>
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156 #end if
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157 #if str($menu_item.menu_url) != "":
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158 <url>${menu_item.menu_url.replace("&", "&amp;").replace("\"", "&quot;")}</url>
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159 #end if
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160 #if str($menu_item.menu_icon) != "":
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161 <iconClass>${menu_item.menu_icon}</iconClass>
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162 #end if
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163 </menu>
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164 #end for
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165 </menus>
3
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166 #end if
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167
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168 #if str($track.data_format.data_format_select) == "wiggle":
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169 <wiggle>
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170 <type>${track.data_format.xyplot}</type>
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171 <variance_band>${track.data_format.var_band}</variance_band>
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172 #if str($track.data_format.scaling.scale_select) == "auto_local":
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173 <autoscale>local</autoscale>
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174 #else if str($track.data_format.scaling.scale_select) == "auto_global":
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175 <autoscale>global</autoscale>
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176 #else:
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177 <min>${track.data_format.scaling.minimum}</min>
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178 <max>${track.data_format.scaling.maximum}</max>
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179 #end if
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180
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181 ## Wiggle tracks need special color config
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182 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
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183 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
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184 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
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185 #else:
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186 <color_pos>__auto__</color_pos>
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187 <color_neg>__auto__</color_neg>
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188 #end if
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189
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190 ## Bicolor pivot config
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191 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
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192 <bicolor_pivot>zero</bicolor_pivot>
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193 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
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194 <bicolor_pivot>mean</bicolor_pivot>
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195 #else:
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196 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
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197 #end if
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198 </wiggle>
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199 #else if str($track.data_format.data_format_select) == "pileup":
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200 <pileup>
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201 <auto_snp>${track.data_format.auto_snp}</auto_snp>
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202 <bam_indices>
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203 #for $dataset in $track.data_format.annotation:
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204 <bam_index>${dataset.metadata.bam_index}</bam_index>
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205 #end for
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206 </bam_indices>
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207 </pileup>
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208 #else if str($track.data_format.data_format_select) == "blast":
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209 <blast>
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210 #if str($track.data_format.blast_parent) != "":
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211 <parent>${track.data_format.blast_parent}</parent>
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212 #end if
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213 <protein>${track.data_format.is_protein}</protein>
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214 <min_gap>${track.data_format.min_gap}</min_gap>
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215 <index>${track.data_format.index}</index>
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216 </blast>
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217 #else if str($track.data_format.data_format_select) == "gene_calls":
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218 <gff>
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219 <trackType>${track.data_format.track_config.track_class}</trackType>
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220 #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures':
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221 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
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222 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
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223 #end if
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224 #if str($track.data_format.track_config.canvas_options.subParts) != "":
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225 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
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226 #end if
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227 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
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228 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
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229 #end if
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230 #end if
3
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231 #if $track.data_format.match_part.match_part_select:
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232 <match>${track.data_format.match_part.name}</match>
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233 #end if
8
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234 <index>${track.data_format.index}</index>
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235 </gff>
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236 ## #else if str($track.data_format.data_format_select) == "sparql":
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237 ## <sparql>
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238 ## <url>${track.data_format.url}</url>
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239 ## <label>${track.data_format.label}</label>
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240 ## <!-- This is going to be an absolutey nightmare -->
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241 ## <query>${track.data_format.query}</query>
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242 ## </sparql>
3
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243 #end if
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244 </options>
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245 </track>
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246 #end for
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247 #end for
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248 </tracks>
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249 </root>
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250 ]]></configfile>
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251 </configfiles>
0
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252 <inputs>
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253 <conditional name="reference_genome">
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254 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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255 <option selected="True" value="indexed">Use a built-in genome</option>
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256 <option value="history">Use a genome from history</option>
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257 </param>
8
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258 <when value="indexed">
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259 <param
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260 help="If your genome of interest is not listed, contact the Galaxy team"
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261 label="Select a reference genome"
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262 name="genomes"
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263 type="select"
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264 >
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265 <options from_data_table="all_fasta">
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266 <filter column="2" type="sort_by" />
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267 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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268 </options>
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269 </param>
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270 </when>
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271 <when value="history">
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272 <param
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273 format="fasta"
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274 label="Select the reference genome"
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275 name="genomes"
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276 type="data"
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277 multiple="True" />
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278 </when>
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279 </conditional>
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280
3
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281 <param name="standalone" label="Produce Standalone Instance" type="boolean" truevalue="Complete" falsevalue="Data Directory" help="Produce a full, working JBrowse instance or just the data directory. Data dir mode is experimental and intended to be used with Apollo" checked="True"/>
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282
8
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283
3
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284 <param label="Genetic Code" name="gencode" type="select">
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285 <option value="1">1. The Standard Code</option>
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286 <option value="2">2. The Vertebrate Mitochondrial Code</option>
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287 <option value="3">3. The Yeast Mitochondrial Code</option>
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288 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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289 <option value="5">5. The Invertebrate Mitochondrial Code</option>
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290 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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291 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
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292 <option value="10">10. The Euplotid Nuclear Code</option>
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293 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
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294 <option value="12">12. The Alternative Yeast Nuclear Code</option>
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295 <option value="13">13. The Ascidian Mitochondrial Code</option>
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296 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
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297 <option value="16">16. Chlorophycean Mitochondrial Code</option>
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298 <option value="21">21. Trematode Mitochondrial Code</option>
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299 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
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300 <option value="23">23. Thraustochytrium Mitochondrial Code</option>
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301 <option value="24">24. Pterobranchia Mitochondrial Code</option>
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302 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
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303 </param>
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304
8
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305 <conditional name="action">
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306 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
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307 <option value="create">New JBrowse Instance</option>
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308 <option value="update">Update exising JBrowse Instance</option>
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309 </param>
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310 <when value="create" />
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311 <when value="update">
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312 <param label="Previous JBrowse Instance"
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313 name="update_jbrowse"
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314 type="data"
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315 format="html" />
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316 </when>
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317 </conditional>
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318
3
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319 <repeat name="track_groups" title="Track Group">
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320 <param label="Track Category"
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321 name="category"
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322 type="text"
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323 value="Default"
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324 help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/>
0
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325 <repeat name="data_tracks" title="Annotation Track">
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326 <conditional name="data_format">
1
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327 <param type="select" label="Track Type" name="data_format_select">
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328 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
1
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329 <option value="pileup">BAM Pileups</option>
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330 <option value="blast">Blast XML</option>
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331 <option value="wiggle">BigWig XY</option>
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332 <option value="vcf">VCF SNPs</option>
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333 <!--<option value="sparql">SPARQL</option>-->
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334 </param>
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335 <when value="blast">
3
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336 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
1
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337
3
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338 <param label="Features used in Blast Search"
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339 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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340 format="gff3"
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341 name="blast_parent"
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342 optional="true"
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343 type="data"/>
1
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344
3
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345 <param label="Minimum Gap Size"
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346 help="before a new match_part feature is created"
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347 name="min_gap"
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348 type="integer"
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349 value="10"
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350 min="2" />
1
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351 <param label="Is this a protein blast search?"
3
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352 type="boolean"
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353 name="is_protein"
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354 truevalue="true"
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355 falsevalue="false" />
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356
8
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357 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
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358
3
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359 <expand macro="track_styling"
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360 classname="feature"
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361 label="description"
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362 description="Hit_titles"
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363 height="600px"/>
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364 <expand macro="color_selection"
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365 token_scaling_lin_select="false"
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366 token_scaling_log_select="true" />
8
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367 <expand macro="track_menu" />
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368 <expand macro="track_display" />
1
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369 </when>
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parents: 0
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370 <when value="vcf">
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parents: 1
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371 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
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parents: 3
diff changeset
372 <expand macro="track_display" />
1
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parents: 0
diff changeset
373 </when>
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parents: 0
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374 <when value="gene_calls">
3
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parents: 1
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375 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
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376 <conditional name="match_part">
3
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parents: 1
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377 <param label="This is match/match_part data"
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parents: 1
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378 type="boolean"
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parents: 1
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379 name="match_part_select"
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parents: 1
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380 truevalue="true"
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parents: 1
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381 falsevalue="false" />
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parents: 1
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382 <when value="true">
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parents: 1
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383 <param label="Match Part Feature Type"
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parents: 1
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384 name="name"
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parents: 1
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385 type="text"
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parents: 1
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386 value="match"
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parents: 1
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387 help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here"
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parents: 1
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388 optional="False"/>
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parents: 1
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389 </when>
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parents: 1
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390 <when value="false" />
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parents: 1
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391 </conditional>
8
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parents: 6
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392
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parents: 6
diff changeset
393 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
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
394
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parents: 8
diff changeset
395 <conditional name="track_config">
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396 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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397 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
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398 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
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parents: 8
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399 </param>
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parents: 8
diff changeset
400 <when value="JBrowse/View/Track/CanvasFeatures">
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
401 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
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parents: 8
diff changeset
402 <param label="Transcript type"
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parents: 8
diff changeset
403 name="transcriptType"
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parents: 8
diff changeset
404 type="text"
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parents: 8
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405 value=""
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parents: 8
diff changeset
406 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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407 optional="True"/>
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
408 <param label="Subfeatures type"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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diff changeset
409 name="subParts"
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parents: 8
diff changeset
410 type="text"
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parents: 8
diff changeset
411 value=""
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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412 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
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413 optional="True"/>
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414 <param label="Implied UTRs"
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
415 name="impliedUTRs"
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
416 type="boolean"
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parents: 8
diff changeset
417 checked="false"
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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parents: 8
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418 truevalue="true"
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419 falsevalue="false"
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parents: 8
diff changeset
420 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"/>
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parents: 8
diff changeset
421 </section>
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parents: 8
diff changeset
422 </when>
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
423 <when value="JBrowse/View/Track/HTMLFeatures" />
1a6d882d340d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
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parents: 8
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424 </conditional>
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parents: 1
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425 <expand macro="track_styling" />
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parents: 1
diff changeset
426 <expand macro="color_selection" />
8
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parents: 6
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427 <expand macro="track_menu" />
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parents: 3
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428 <expand macro="track_display" />
1
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parents: 0
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429 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
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430 <when value="pileup">
3
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parents: 1
diff changeset
431 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
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parents: 1
diff changeset
432 <param label="Autogenerate SNP Track"
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parents: 1
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433 help="Not recommended for deep coverage BAM files"
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parents: 1
diff changeset
434 type="boolean"
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parents: 1
diff changeset
435 name="auto_snp"
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parents: 1
diff changeset
436 truevalue="true"
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parents: 1
diff changeset
437 falsevalue="false" />
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parents: 3
diff changeset
438 <expand macro="track_display" />
1
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parents: 0
diff changeset
439 </when>
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440 <when value="wiggle">
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parents: 1
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441 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
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parents: 1
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442
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parents: 1
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443 <param label="Use XYPlot"
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parents: 1
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444 help="instead of continuous colored band"
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parents: 1
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445 type="boolean"
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parents: 1
diff changeset
446 name="xyplot"
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parents: 1
diff changeset
447 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
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parents: 1
diff changeset
448 falsevalue="JBrowse/View/Track/Wiggle/Density" />
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
449 <param label="Show variance band"
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parents: 1
diff changeset
450 help="Only for XYPlots"
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parents: 1
diff changeset
451 type="boolean"
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parents: 1
diff changeset
452 name="var_band"
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parents: 1
diff changeset
453 truevalue="true"
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parents: 1
diff changeset
454 falsevalue="false" />
1
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parents: 0
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455
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parents: 6
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456 <conditional name="scaling">
1
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parents: 0
diff changeset
457 <param type="select" label="Track Scaling" name="scale_select">
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458 <option value="auto_local">Autoscale (local)</option>
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parents: 1
diff changeset
459 <option value="auto_global" selected="true">Autoscale (global)</option>
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parents: 1
diff changeset
460 <option value="fixed">Specify Min/Max</option>
1
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parents: 0
diff changeset
461 </param>
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parents: 0
diff changeset
462 <when value="auto_local"></when>
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parents: 0
diff changeset
463 <when value="auto_global"></when>
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parents: 0
diff changeset
464 <when value="fixed">
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
465 <param label="Track minimum" name="minimum"
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
466 type="integer" value="0" />
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
467 <param label="Track maximum" name="maximum"
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
468 type="integer" value="100" />
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
469 </when>
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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parents: 0
diff changeset
470 </conditional>
3
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parents: 1
diff changeset
471 <expand macro="color_selection_minmax" />
5
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parents: 3
diff changeset
472 <expand macro="track_display" />
1
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parents: 0
diff changeset
473 </when>
5
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parents: 3
diff changeset
474 <!--
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
475 <when value="sparql">
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
476 <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
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parents: 3
diff changeset
477 <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
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parents: 3
diff changeset
478 <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
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parents: 3
diff changeset
479 <expand macro="track_display" />
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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parents: 3
diff changeset
480 </when>
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
481 -->
1
497c6bb3b717 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents: 0
diff changeset
482 </conditional>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
483 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
484 </repeat>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
485
5
ae9382cfb6ac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents: 3
diff changeset
486 <expand macro="general_options" />
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
487 <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
488 </inputs>
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
489 <outputs>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
490 <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
491 </outputs>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
492 <tests>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
493 <test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
494 <!-- gencode -->
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
495 <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
496 <param name="reference_genome|genomes" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
497 <param name="gencode" value="1" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
498 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
499 <param name="uglyTestingHack" value="enabled" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
500 <output name="output" file="gencode/test-1.xml" lines_diff="4" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
501 </test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
502 <test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
503 <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
504 <param name="reference_genome|genomes" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
505 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
506 <param name="standalone" value="Data Directory" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
507 <param name="uglyTestingHack" value="enabled" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
508 <output name="output" file="gencode/test.xml" lines_diff="4"/>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
509 </test>
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
510 <test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
511 <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
512 <param name="reference_genome|genomes" value="merlin.fa"/>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
513 <param name="gencode" value="11" />
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
514 <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
515 <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
516 <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
517 <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
518 <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
519 <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
520 <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
521 <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
522 <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
523 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
524 <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
525 <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
526 <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
527 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
528 <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
529 <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
530 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
531 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
532 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
533 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
534 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
535
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
536 <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
537 <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
538 <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
539 <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
540 <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
541 <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
542 <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
543 <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
544 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
545 <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
546 <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
547 <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
548 <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
549 <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
550 <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
551 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
552 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
553 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
554 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
555 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
556 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
557
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
558 <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
559 <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
560 <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
561 <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
562 <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
563 <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
564 <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
565 <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
566 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
567 <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
568 <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
569 <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
570 <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
571 <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
572 <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
573 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
574 <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
575 <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
576 <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
577 <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
578 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
579 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
580 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
581 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
582 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
583 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
584 <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
585 <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
586 <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
587 <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
588 <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
589 <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
590 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
591 <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
592 <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
593 <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
594 <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
595 <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
596 <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
597 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
598 <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
599 <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
600 <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
601 <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
602 <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
603 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
604 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
605 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
606 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
607 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
608 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
609 <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
610 <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
611 <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
612 <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
613 <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
614 <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
615 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
616 <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
617 <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
618 <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
619 <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
620 <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
621 <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
622 <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
623 <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
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_scheme">
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="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
627 <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
628 <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
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 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
631 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
632 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
633 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
634 </repeat>
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="score"/>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
645 <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
646 <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
647 <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
648 <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
649 <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
650 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
651 <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
652 <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
653 <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
654 <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
655 <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
656 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
657 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
658 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
659 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
660 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
661 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
662 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
663
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
664 <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
665 <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
666 <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
667 <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
668 <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
669 <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
670 <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
671 <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
672 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
673 <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
674 <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
675 <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
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 name="color">
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
678 <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
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 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
681 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
682 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
683 <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
684 <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
685 <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
686 <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
687 <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
688 <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
689 <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
690 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
691 <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
692 <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
693 <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
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">
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="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
697 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
698 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
699 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
700 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
701 </repeat>
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
702
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
703 <param name="uglyTestingHack" value="enabled" />
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
704 <output name="output" file="gff3/test.xml" lines_diff="24" />
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
705 </test>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
706 <test>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
707 <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
708 <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
709 <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
710 <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
711
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
712 <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
713 <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
714 <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
715 <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
716 <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
717 <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
718 <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
719 <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
720 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
721 <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
722 <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
723 <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
724 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
725 <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
726 <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
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 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
729 <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
730 <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
731 <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
732 <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
733 <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
734 <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
735 <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
736 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
737 <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
738 <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
739 <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
740 <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
741 <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
742 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
743 </section>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
744 </conditional>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
745 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
746 <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
747 <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
748 <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
749 <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
750 <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
751 <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
752 <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
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 <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
755 <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
756 <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
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 <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
759 <param name="color_select" value="automatic"/>
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diff changeset
760 </conditional>
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diff changeset
761 </section>
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diff changeset
762 </conditional>
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diff changeset
763 </repeat>
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff changeset
764 </repeat>
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diff changeset
765
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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diff changeset
766 <param name="uglyTestingHack" value="enabled" />
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diff changeset
767 <output name="output" file="menus/test.xml" lines_diff="6"/>
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diff changeset
768 </test>
10
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diff changeset
769 <test>
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diff changeset
770 <param name="reference_genome|genome_type_select" value="history"/>
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diff changeset
771 <param name="reference_genome|genomes" value="merlin.fa"/>
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diff changeset
772 <param name="gencode" value="11" />
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diff changeset
773 <param name="standalone" value="Data Directory" />
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diff changeset
774
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diff changeset
775 <repeat name="track_groups">
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diff changeset
776 <param name="category" value="With canvas config" />
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diff changeset
777 <repeat name="data_tracks">
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diff changeset
778 <conditional name="data_format">
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diff changeset
779 <param name="data_format_select" value="gene_calls"/>
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diff changeset
780 <param name="annotation" value="gff3/1.gff"/>
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diff changeset
781 <conditional name="match_part">
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diff changeset
782 <param name="match_part_select" value="false"/>
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783 </conditional>
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diff changeset
784 <conditional name="track_config">
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diff changeset
785 <section name="canvas_options">
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diff changeset
786 <param name="transcriptType" value="transcript"/>
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diff changeset
787 <param name="subParts" value="exon"/>
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diff changeset
788 <param name="impliedUTRs" value="true"/>
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diff changeset
789 </section>
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790 </conditional>
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diff changeset
791 <section name="jbcolor_scale">
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diff changeset
792 <conditional name="color_score">
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diff changeset
793 <param name="color_score_select" value="none"/>
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diff changeset
794 </conditional>
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diff changeset
795 <conditional name="color">
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diff changeset
796 <param name="color_select" value="automatic"/>
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diff changeset
797 </conditional>
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diff changeset
798 </section>
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799 </conditional>
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800 </repeat>
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801 </repeat>
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diff changeset
802
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diff changeset
803 <param name="uglyTestingHack" value="enabled" />
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diff changeset
804 <output name="output" file="track_config/test.xml" lines_diff="6"/>
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diff changeset
805 </test>
3
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diff changeset
806 </tests>
0
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diff changeset
807 <help><![CDATA[
3
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diff changeset
808 JBrowse-in-Galaxy
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diff changeset
809 =================
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diff changeset
810
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diff changeset
811 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
812 alternative to Trackster.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
813
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
814 The JBrowse-in-Galaxy (JiG) tool was written to help build complex
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diff changeset
815 JBrowse installations straight from Galaxy, taking advantage of the
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
816 latest Galaxy features such as dataset collections, sections, and colour
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
817 pickers. It allows you to build up a JBrowse instance without worrying
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
818 about how to run the command line tools to format your data, and which
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diff changeset
819 options need to be supplied and where. Additionally it comes with many
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
820 javascript functions to handle colouring of features which would be
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
821 nearly impossible to write without the assistance of this tool.
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
822
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diff changeset
823 The JBrowse-in-Galaxy tool is maintained by `Eric
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parents: 1
diff changeset
824 Rasche <mailto:esr+jig@tamu.edu>`__, who you can contact if you
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diff changeset
825 encounter missing features or bugs.
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diff changeset
826
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diff changeset
827 Options
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diff changeset
828 -------
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
829
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830 The first option you encounter is the **Fasta Sequence(s)**. This option
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diff changeset
831 now accepts multiple fasta files, allowing you to build JBrowse
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
832 instances that contain data for multiple genomes or chrosomomes
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diff changeset
833 (generally known as "landmark features" in gff3 terminology.) Up to 30
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diff changeset
834 will be shown from the dropdown selector within JBrowse, this is a known
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diff changeset
835 issue.
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diff changeset
836
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diff changeset
837 **Standalone Instances** are a somewhat in-development feature.
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diff changeset
838 Currently Galaxy copies the entire JBrowse directory in order to have a
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
839 complete, downloadable file that contains a ready-to-go JBrowse
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
840 instance. This is obviously an anti-feature because users don't want a
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
841 complete copy of JBrowse (6-20Mb) that's duplicated for every JBrowse
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
842 dataset in their history, and admins don't want useless copies of
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diff changeset
843 JBrowse on disk. Unfortunately we have not come up with the perfect
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diff changeset
844 solution just yet, but we're working on it! In the meantime, users have
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diff changeset
845 been given the option to produce just the ``data/`` directory. For those
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
846 unfamiliar with JBrowse, the ``data/`` directory contains processed data
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diff changeset
847 files, but no way to view them. This feature is additionally implemented
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
848 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration.
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
849
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diff changeset
850 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse,
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diff changeset
851 which allows users to specify a non standard genetic code, and have
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
852 JBrowse highlight the correct start and stop codons. If you would like
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
853 to use a coding table not provided by this list, please let
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
854 `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
855 this.
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diff changeset
856
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diff changeset
857 **Track Groups** represent a set of tracks in a single category. These
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
858 can be used to let your users understand relationships between large
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diff changeset
859 groups of tracks.
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diff changeset
860
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diff changeset
861 .. image:: sections.png
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diff changeset
862
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diff changeset
863 Annotation Tracks
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iuc
parents: 1
diff changeset
864 -----------------
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
865
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diff changeset
866 Within Track Groups, you have one or more **Annotation Tracks**. Each
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
867 Annotation Track is a groups of datasets which have similar styling.
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diff changeset
868 This allows you to rapidly build up JBrowse instances without having to
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
869 configure tracks individually. A massive improvement over previous
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
870 versions. For example, if you have five different GFF3 files from
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
871 various gene callers that you wish to display, you can take advantage of
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
872 this feature to style all of them similarly.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
873
7342f467507b Uploaded v0.4 of JBrowse
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diff changeset
874 There are a few different types of tracks supported, each with their own
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
875 set of options:
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
876
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
877 GFF3/BED/GBK
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
878 ~~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
879
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
880 These are your standard feature tracks. They usually highlight genes,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
881 mRNAs and other features of interest along a genomic region. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
882 underlying tool and this help documentation focus primarily on GFF3
7342f467507b Uploaded v0.4 of JBrowse
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parents: 1
diff changeset
883 data, and have not been tested extensively with other formats. Automatic
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
884 min/max detection will likely fail under BED and GBK datasets.
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
885
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
886 The data may be of a subclass we call **match/match part** data. This
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iuc
parents: 1
diff changeset
887 consists of top level ``match`` features, with a child ``match_part``
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
888 feature, and is often used in displaying alignments. (See "Alignments"
7342f467507b Uploaded v0.4 of JBrowse
iuc
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diff changeset
889 section on the `GFF3
8
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diff changeset
890 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more
3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
891 information). If the data is match/match part, you will need to specify
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
892 the top level match feature name, as it can be one of a few different SO
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
893 terms, and JiG does not yet have the ability to understand SO terms.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
894
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
895 Next up is the **Styling Options** section, which lets you control a few
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
896 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
897 to configure and can safely leave on defaults. Occasionally you will
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
898 want to change what information is shown in the end product.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
899
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
900 .. image:: styling.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
901
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
902 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
903 source of the black text is configured with the **style.label** option,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
904 and the source of the blue text is configured with the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
905 **style.description** option.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
906
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
907 Feature Score Scaling & Colouring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
908 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
909
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
910 First, you need to choose between ignoring the score attribute of GFF3
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
911 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
912 coloured with a solid colour. If you choose to use it, features will
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
913 have slightly different colours based on their scores.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
914
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
915 .. image:: opacity.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
916
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
917 If you choose **Ignore score**, you may choose between automatically
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
918 choosing a colour, or manually specifying one. The automatically chosen
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
919 colours vary along a brewer palette and generally look quite nice with
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
920 no human intervention required. The manual colour choice is somewhat
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
921 self explanatory. Clicking on the small coloured square will bring up a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
922 colour palette.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
923
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
924 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
925 options. First is the function to map the colour choices to colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
926 values. JiG comes with a few functions built in such as linear scaling,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
927 logarithmic scaling, and blast scaling.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
928
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
929 The **linear scaling** method says "take these values, and they map
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
930 directly to a range of output values". **Logarithmic scaling** says
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
931 "please take the log of the score before mapping", and **Blast scaling**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
932 is further specialised to handle blast data more nicely. These are
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
933 convenience functions to help transform the wide array of possible
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
934 values in the GFF3 score attribute to more meaningful numbers. If you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
935 need more comprehensive score scaling, it is recommended that you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
936 pre-process your GFF3 files somehow.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
937
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
938 Once you've selected a scaling method, you can choose to manually
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
939 specify the minimum and maximum expected values, or you can let JiG
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
940 determine them for you automatically.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
941
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
942 Finally, opacity is the only mapping we currently provide. Future
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
943 iterations will attempt to improve upon this and provide more colour
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
944 scales. The Opacity option maps the highest scoring features to full
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
945 opacity, and everything else to lower ones.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
946
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
947 BAM Pileups
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
948 ~~~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
949
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
950 We support BAM files and can automatically generate SNP tracks based on
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
951 that bam data.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
952
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
953 .. image:: bam.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
954
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
955 This is *strongly discouraged* for high coverage density datasets.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
956 Unfortunately there are no other configuration options exposed for bam
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
957 files. If you find JBrowse options you wish to see exposed, please let
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
958 `me <mailto:esr+jig@tamu.edu>`__ know.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
959
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
960 BlastXML
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
961 ~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
962
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
963 .. image:: blast.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
964
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
965 JiG now supports both blastn and blastp datasets. JiG internally uses a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
966 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
967 format amenable to visualization in JBrowse. This tool is also
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
968 available separately from the IUC on the toolshed.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
969
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
970 **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
971 real gap in the processed gff3 file. In the picture above, various sizes
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
972 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
973 100nt, many of the smaller gaps would disappear, and the features on
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
974 both sides would be merged into one, longer feature. This setting is
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
975 inversely proportional to runtime and output file size. *Do not set this
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
976 to a low value for large datasets*. By setting this number lower, you
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
977 will have extremely large outputs and extremely long runtimes. The
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
978 default was configured based off of the author's experience, but the
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
979 author only works on small viruses. It is *strongly* recommended that
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
980 you filter your blast results before display, e.g. picking out the top
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
981 10 hits or so.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
982
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
983 **Protein blast search** option merely informs underlying tools that
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
984 they should adjust feature locations by 3x.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
985
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
986 Styling Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
987 ^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
988
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
989 Please see the styling options for GFF3 datasets, they are identical.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
990
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
991 Feature Score Scaling & Coloring Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
992 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
993
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
994 Please see the score scaling and colouring options for GFF3 datasets,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
995 they are identical. Remember to set your score scaling to "blast" method
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
996 if you do use it.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
997
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
998 Bigwig XY
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
999 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1000
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1001 .. image:: bigwig.png
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1002
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1003 **XYPlot**
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1004
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1005 BigWig tracks can be displayed as a "density" plot which is continuous
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1006 line which varies in colour, or as an "XYplot." XYplots are preferable
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1007 for users to visually identify specific features in a bigwig track,
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1008 however density tracks are more visually compact.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1009
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1010 **Variance Band** is an option available to XYPlots, and can be seen in
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1011 the third and fourth tracks in the above picture. This overlays a mean
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1012 line, and 1 and 2 standard deviation areas.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1013
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1014 **Track Scaling** is different from colour scaling, instead it
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1015 configures how the track behaves inside of JBrowse. **Autoscaling
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1016 globally** means that JBrowse will determine the minimum and maximum for
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1017 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
1018 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
1019 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
1020 good for global genomic context. However you may wish to consider
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1021 **autoscaling locally** instead. In the example of a region which varies
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1022 from 0-50, autoscaling locally would cause the individual track's
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1023 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
1024 options are palatable, you may manually hardcode the minimum and
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1025 maximums for the track to scale to.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1026
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1027 Colour Options
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1028 ^^^^^^^^^^^^^^
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1029
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1030 BigWig tracks have two colours in JBrowse, a positive and a negative
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1031 colour.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1032
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1033 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
1034
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1035 One of the more interesting options is the **Bicolor pivot**. This
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1036 option allows you to control the point at which JBrowse switches from
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1037 the positive colour to the negative. In the above graphic, you can see
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1038 this has been configured to "mean" for the first two (orange and blue)
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1039 tracks.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1040
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1041 VCFs/SNPs
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1042 ~~~~~~~~~
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1043
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1044 These tracks do not support any special configuration.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1045
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1046 Known Issues
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1047 ------------
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1048
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1049 - More than 30 landmark features cannot be listed in the manual
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1050 selector.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1051 - Non GFF3 likely has issue with automatically determined min/max
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1052 scores. Manually specify minimum and maximum score attributes, or do
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1053 not use varied colours based on scores to avoid this issue.
7342f467507b Uploaded v0.4 of JBrowse
iuc
parents: 1
diff changeset
1054
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1055
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1056 @ATTRIBUTION@
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff changeset
1057 ]]></help>
8
ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 6
diff changeset
1058 <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
1059 </tool>