Mercurial > repos > iuc > jbrowse

annotate macros.xml @ 54:b4d512ee2d14 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
author iuc
date Tue, 19 Feb 2019 15:42:56 -0500
parents c6fd9fbd50e7
children 61a47bf57b3e
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.16.2</token>
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4 <xml name="requirements">
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5 <requirements>
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6 <requirement type="package" version="@TOOL_VERSION@">jbrowse</requirement>
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7 <requirement type="package" version="2.7">python</requirement>
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8 <requirement type="package" version="1.72">biopython</requirement>
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9 <requirement type="package" version="0.6.4">bcbiogff</requirement>
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10 <requirement type="package" version="1.9">samtools</requirement>
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11 <requirement type="package" version="3.13">pyyaml</requirement>
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12 <requirement type="package" version="0.2.6">tabix</requirement>
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13 <yield/>
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14 </requirements>
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15 </xml>
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16 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
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17 <token name="@WRAPPER_VERSION@">galaxy0</token>
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18 <token name="@ATTRIBUTION@"><![CDATA[
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19 **Attribution**
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20
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21 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
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22 ]]>
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23 </token>
45
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24
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25 <xml name="genome_selector"
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26 token_help=""
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27 token_label="Fasta sequences"
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28 token_optional="False" >
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29 <conditional name="reference_genome">
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30 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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31 <option selected="True" value="indexed">Use a built-in genome</option>
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32 <option value="history">Use a genome from history</option>
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33 </param>
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34 <when value="indexed">
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35 <param
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36 help="@HELP@"
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37 label="@LABEL@"
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38 name="genomes"
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39 type="select"
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40 optional="@OPTIONAL@"
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41 >
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42 <options from_data_table="all_fasta">
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43 <filter column="2" type="sort_by" />
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44 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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45 </options>
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46 </param>
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47 </when>
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48 <when value="history">
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49 <param
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50 format="fasta"
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51 label="@LABEL@"
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52 help="@HELP@"
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53 name="genomes"
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54 type="data"
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55 optional="@OPTIONAL@"
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56 multiple="True" />
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57 </when>
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58 </conditional>
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59 </xml>
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60
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61 <xml name="auto_manual_tk"
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62 token_cond_label="Color"
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63 token_cond_name="color"
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64 token_select_label="Color Specification"
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65 token_select_name="color_select"
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66 token_automatic_label="Automatically selected"
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67 token_manual_label="Manual Color Selection">
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68 <conditional name="@COND_NAME@" label="@COND_LABEL@">
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69 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
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70 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
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71 <option value="manual">@MANUAL_LABEL@</option>
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72 </param>
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73 <when value="automatic">
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74 </when>
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75 <when value="manual">
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76 <yield />
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77 </when>
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78 </conditional>
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79 </xml>
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80
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81 <xml name="track_display">
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82 <param type="select" label="Track Visibility" name="track_visibility">
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83 <option value="default_off">Off for new users</option>
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84 <option value="default_on">On for new users</option>
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85 <option value="force">Force On</option>
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86 <option value="always">Always On (ignores URL parameters)</option>
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87 </param>
45
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88 <param type="select" label="Override Apollo Plugins" name="override_apollo_plugins" help="Disable the apollo plugin for this track, this disables the ability to make an annotation from this feature.">
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89 <option value="True">Yes - Override</option>
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90 <option value="False" selected="True">No - Do not Override</option>
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91 </param>
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92 <param type="select" label="Override Apollo Draggability" name="override_apollo_drag" help="Disable apollo's drag-to-create feature functionality.">
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93 <option value="True">Yes - Override</option>
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94 <option value="False" selected="True">No - Do not Override</option>
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95 </param>
30
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96 </xml>
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97
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98 <xml name="jb_color"
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99 token_label="JBrowse style.color"
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100 token_name="style_color"
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101 token_value="goldenrod"
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102 token_help="Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS"
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103 >
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104 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
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105 <sanitizer>
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106 <valid initial="string.letters,string.digits">
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107 <add value="#" />
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108 </valid>
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109 </sanitizer>
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110 </param>
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111 </xml>
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112
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113 <xml name="auto_color"
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114 token_cond_label="Color"
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115 token_cond_name="color"
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116 token_select_label="Color Selection"
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117 token_select_name="color_select"
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118 token_automatic_label="Automatically selected"
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119 token_manual_label="Manual Color Selection">
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120 <expand macro="auto_manual_tk"
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121 cond_label="@COND_LABEL@"
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122 cond_name="@COND_NAME@"
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123 select_label="@SELECT_LABEL@"
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124 select_name="@SELECT_NAME@"
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125 automatic_label="@AUTOMATIC_LABEL@"
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126 manual_label="@MANUAL_LABEL@">
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127 <expand macro="jb_color" />
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128 <yield />
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129 </expand>
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130 </xml>
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131
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132
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133
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134 <xml name="brewer_scheme">
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135 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
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136 <option value="BrBg">BrBg: Brown - Blue Green</option>
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137 <option value="PiYg">PiYg: Pink - Yellow Green</option>
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138 <option value="PRGn">PRGn: Purple Red - Green</option>
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139 <option value="PuOr">PuOr: Purple - Orange</option>
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140 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
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141 <option value="RdGy">RdGy: Red - Gray</option>
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142 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
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143 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
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144 <option value="Spectral">Spectral</option>
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145 </param>
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146 </xml>
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147 <xml name="general_options">
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148 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
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149 <param label="Default Location" type="text" name="defaultLocation" value="" help="Initial location to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678'"/>
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150 <param label="Track Padding" type="integer" value="20" name="trackPadding" help="Spacing between tracks in the genome view, in pixels." />
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151
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152 <param label="Enable Share Link" name="shareLink" type="boolean" checked="true" truevalue="true" falsevalue="false" />
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153 <param label="About the Browser" type="text" name="aboutDescription" value="" help="Description of the browser to be used in the 'About' popup" />
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154
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155 <param label="Show Track List" name="show_tracklist" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the track list"/>
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156 <param label="Show Navigation" name="show_nav" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the navigation menu"/>
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157 <param label="Show Overview" name="show_overview" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the overview bar"/>
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158 <param label="Show Menu" name="show_menu" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the menu bar"/>
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159
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160 <param label="Hide Genome Options" name="hideGenomeOptions" type="boolean" truevalue="true" falsevalue="false" help="Hide options for opening a sequence file"/>
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161 </section>
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162 </xml>
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163 <xml name="color_selection_minmax">
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164 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
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165 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
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166 auto case as well, but may be safe to just say "brewer colors? Pff,
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167 red/blue" -->
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168 <expand macro="auto_manual_tk"
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169 token_cond_label="Color"
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170 token_cond_name="color"
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171 token_select_label="Color Selection"
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172 token_select_name="color_select"
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173 token_automatic_label="Automatically selected"
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174 token_manual_label="Manual Color Selection">
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175 <expand macro="jb_color"
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176 label="JBrowse style.pos_color"
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177 name="style_pos_color"
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178 value="blue"
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179 help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." />
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180 <expand macro="jb_color"
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181 label="JBrowse style.neg_color"
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182 name="style_neg_color"
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183 value="red"
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184 help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." />
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185 </expand>
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186
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187 <conditional name="bicolor_pivot" label="Bicolor Pivot">
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188 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
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189 <option value="zero" selected="true">Zero</option>
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190 <option value="mean">Mean</option>
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191 <option value="custom">Custom Value</option>
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192 </param>
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193 <when value="zero" />
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194 <when value="mean" />
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195 <when value="custom">
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196 <param label="JBrowse style.bicolor_pivot" type="float" name="pivot_point" value="0.0" help="Where to change from pos_color to neg_color when drawing bicolor plots." />
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197 </when>
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198 </conditional>
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199 </section>
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200 </xml>
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201
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202 <xml name="color_selection"
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203 token_scaling_lin_select="true"
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204 token_scaling_log_select="false"
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205 >
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206 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
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207 <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
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208 <param type="select" label="Color Score Algorithm" name="color_score_select" help="How to color the features. If it is based on score, then features with a score attribute anywhere in their hierachy will have their color affected by the score. If you choose to ignore the score, then you'll be able to select a single solid color for every feature in the track">
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209 <option value="score">Based on score</option>
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210 <option value="none" selected="true">Ignore score</option>
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211 </param>
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212 <when value="none">
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213 <!-- When no scaling is done, no scores available, then just let the
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214 user choose a base color for the track -->
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215 <expand macro="auto_color" />
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216 </when>
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217 <when value="score">
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218 <!-- Scaling -->
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219 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
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220 help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution.">
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221 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option>
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222 <option value="logarithmic" selected="false">Logarithmic scaling</option>
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223 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
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224 </param>
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225
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226 <!-- Scaling Bounds -->
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227 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
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228 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select">
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229 <option value="automatic" selected="true">Automatically determined</option>
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230 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
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231 </param>
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232 <when value="automatic">
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233 </when>
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234 <when value="manual">
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235 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
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236 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
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237 </when>
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238 </conditional>
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239
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240 <!-- Scale color -->
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241 <conditional name="color_scheme" label="Color Scheme for scored features">
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242 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme">
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243 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
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244 <!--<option value="brewer">Brewer Color Schemes</option>-->
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245 </param>
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246 <when value="opacity">
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247 <!-- Single color selection mode -->
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248 <expand macro="auto_color" />
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249 </when>
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250 <!--<when value="brewer">-->
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251 <!--[> Brewer continuum selection <]-->
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252 <!--<expand macro="brewer_scheme" />-->
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253 <!--</when>-->
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254 </conditional>
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255 </when>
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256 </conditional>
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257 </section>
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258 </xml>
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259 <xml name="track_styling"
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260 token_classname="feature"
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261 token_label="product,name,id"
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262 token_description="note,description"
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263 token_height="10px"
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264 token_maxheight="600">
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265 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
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266 <param label="JBrowse style.className" type="text"
29
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267 name="style_classname"
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268 value="@CLASSNAME@"
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269 help="Set CSS style.className property"/>
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270 <param label="JBrowse style.label"
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271 type="text"
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272 name="style_label"
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273 value="@LABEL@"
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274 help="Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'" />
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275 <param label="JBrowse style.description"
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276 type="text"
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277 name="style_description"
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278 value="@DESCRIPTION@"
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279 help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/>
16
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280 <param label="JBrowse style.height"
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281 type="text"
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282 name="style_height"
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283 value="@HEIGHT@"
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284 help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/>
45
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285 <param label="JBrowse maxHeight"
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286 type="text"
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287 name="max_height"
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288 value="@MAXHEIGHT@"
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289 help="Maximum height that the track is permitted to reach in pixels."/>
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290 </section>
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291 </xml>
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292
42
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293 <xml name="track_menu">
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294 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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295 <repeat name="track_menu" title="Track Menu">
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296 <param label="Menu action"
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297 type="select"
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298 name="menu_action"
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299 help="Action performed when user clicks on the menu">
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300 <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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301 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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302 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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303 </param>
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iuc
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304 <param label="Menu label"
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305 type="text"
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306 name="menu_label"
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307 help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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308 <expand macro="menu_sanitize" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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309 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
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310 <param label="Menu title"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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311 type="text"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
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312 name="menu_title"
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iuc
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313 help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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314 <expand macro="menu_sanitize" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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315 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
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316 <param label="Menu url"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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317 type="text"
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iuc
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318 name="menu_url"
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319 help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
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320 <expand macro="menu_sanitize" />
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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321 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
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322 <param label="Menu icon"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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323 type="select"
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324 name="menu_icon"
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325 help="Icon to display next to menu label">
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326 <option value="dijitIconBookmark" selected="true">Bookmark</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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327 <option value="dijitIconSave">Save</option>
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328 <option value="dijitIconPrint">Print</option>
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329 <option value="dijitIconCut">Cut</option>
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330 <option value="dijitIconCopy">Copy</option>
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331 <option value="dijitIconClear">Clear</option>
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332 <option value="dijitIconDelete">Delete</option>
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333 <option value="dijitIconUndo">Undo</option>
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334 <option value="dijitIconEdit">Edit</option>
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335 <option value="dijitIconNewTask">New Task</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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336 <option value="dijitIconEditTask">Edit Task</option>
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337 <option value="dijitIconEditProperty">Edit Property</option>
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338 <option value="dijitIconTask">Task</option>
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339 <option value="dijitIconFilter">Filter</option>
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340 <option value="dijitIconConfigure">Configure</option>
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341 <option value="dijitIconSearch">Search</option>
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342 <option value="dijitIconApplication">Application</option>
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343 <option value="dijitIconChart">Chart</option>
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344 <option value="dijitIconConnector">Connector</option>
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345 <option value="dijitIconDatabase">Database</option>
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346 <option value="dijitIconDocuments">Documents</option>
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347 <option value="dijitIconMail">Mail</option>
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348 <option value="dijitLeaf">Leaf</option>
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349 <option value="dijitIconFile">File</option>
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350 <option value="dijitIconFunction">Function</option>
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351 <option value="dijitIconKey">Key</option>
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352 <option value="dijitIconPackage">Package</option>
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353 <option value="dijitIconSample">Sample</option>
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354 <option value="dijitIconTable">Table</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
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355 <option value="dijitIconUsers">Users</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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356 <option value="dijitIconFolderClosed">Folder Closed</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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357 <option value="dijitIconFolderOpen">Folder Open</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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358 <option value="dijitIconError">Error</option>
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359 </param>
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360 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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361 </section>
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362 </xml>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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363
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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diff changeset
364 <xml name="menu_sanitize">
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diff changeset
365 <sanitizer>
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366 <valid>
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367 <add value="{"/>
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368 <add value="}"/>
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369 <add value="!"/>
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370 <add value="?"/>
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371 <add value="&amp;"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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372 <add value="+"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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373 <add value="="/>
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374 <add value="'"/>
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375 <add value='"'/>
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376 </valid>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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377 </sanitizer>
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378 </xml>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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379
16
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380 <xml name="input_conditional" token_label="Track Data" token_format="data">
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381 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
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382 </xml>
42
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383 <xml name="citations">
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384 <citations>
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385 <citation type="doi">10.1101/gr.094607.109</citation>
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386 </citations>
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387 </xml>
0
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388 </macros>