Mercurial > repos > iuc > jbrowse

annotate macros.xml @ 73:0745b27fe62c draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 80fbf6800feb0bb02c047d37e97b7a12e9c68f4c"
author iuc
date Fri, 23 Apr 2021 11:36:56 +0000
parents b4c1bf3bbe20
children
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.16.11</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 <requirement type="package" version="4.6.0">findutils</requirement>
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14 <yield/>
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15 </requirements>
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16 </xml>
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17 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
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18 <token name="@WRAPPER_VERSION@">galaxy1</token>
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19 <token name="@ATTRIBUTION@"><![CDATA[
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20 **Attribution**
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21
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22 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC
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23 ]]>
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24 </token>
45
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25
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26 <xml name="genome_selector"
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27 token_help=""
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28 token_label="Fasta sequences"
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29 token_optional="False" >
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30 <conditional name="reference_genome">
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31 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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32 <option selected="True" value="indexed">Use a built-in genome</option>
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33 <option value="history">Use a genome from history</option>
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34 </param>
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35 <when value="indexed">
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36 <param
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37 help="@HELP@"
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38 label="@LABEL@"
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39 name="genomes"
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40 type="select"
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41 optional="@OPTIONAL@"
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42 >
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43 <options from_data_table="all_fasta">
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44 <filter column="2" type="sort_by" />
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45 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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46 </options>
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47 </param>
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48 </when>
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49 <when value="history">
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50 <param
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51 format="fasta"
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52 label="@LABEL@"
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53 help="@HELP@"
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54 name="genomes"
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55 type="data"
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56 optional="@OPTIONAL@"
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57 multiple="True" />
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58 </when>
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59 </conditional>
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60 </xml>
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61
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62 <xml name="auto_manual_tk"
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63 token_cond_label="Color"
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64 token_cond_name="color"
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65 token_select_label="Color Specification"
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66 token_select_name="color_select"
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67 token_automatic_label="Automatically selected"
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68 token_manual_label="Manual Color Selection">
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69 <conditional name="@COND_NAME@" label="@COND_LABEL@">
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70 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
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71 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
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72 <option value="manual">@MANUAL_LABEL@</option>
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73 </param>
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74 <when value="automatic">
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75 </when>
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76 <when value="manual">
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77 <yield />
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78 </when>
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79 </conditional>
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80 </xml>
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81
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82 <xml name="track_display">
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83 <param type="select" label="Track Visibility" name="track_visibility">
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84 <option value="default_off">Off for new users</option>
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85 <option value="default_on">On for new users</option>
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86 <option value="force">Force On</option>
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87 <option value="always">Always On (ignores URL parameters)</option>
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88 </param>
45
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89 <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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90 <option value="True">Yes - Override</option>
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91 <option value="False" selected="True">No - Do not Override</option>
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92 </param>
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93 <param type="select" label="Override Apollo Draggability" name="override_apollo_drag" help="Disable apollo's drag-to-create feature functionality.">
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94 <option value="True">Yes - Override</option>
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95 <option value="False" selected="True">No - Do not Override</option>
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96 </param>
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97 </xml>
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98
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99 <xml name="jb_color"
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100 token_label="JBrowse style.color"
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101 token_name="style_color"
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102 token_value="goldenrod"
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103 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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104 >
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105 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
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106 <sanitizer>
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107 <valid initial="string.letters,string.digits">
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108 <add value="#" />
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109 </valid>
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110 </sanitizer>
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111 </param>
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112 </xml>
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113
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114 <xml name="auto_color"
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115 token_cond_label="Color"
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116 token_cond_name="color"
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117 token_select_label="Color Selection"
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118 token_select_name="color_select"
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119 token_automatic_label="Automatically selected"
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120 token_manual_label="Manual Color Selection">
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121 <expand macro="auto_manual_tk"
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122 cond_label="@COND_LABEL@"
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123 cond_name="@COND_NAME@"
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124 select_label="@SELECT_LABEL@"
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125 select_name="@SELECT_NAME@"
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126 automatic_label="@AUTOMATIC_LABEL@"
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127 manual_label="@MANUAL_LABEL@">
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128 <expand macro="jb_color" />
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129 <yield />
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130 </expand>
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131 </xml>
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132
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133
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134
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135 <xml name="brewer_scheme">
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136 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
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137 <option value="BrBg">BrBg: Brown - Blue Green</option>
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138 <option value="PiYg">PiYg: Pink - Yellow Green</option>
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139 <option value="PRGn">PRGn: Purple Red - Green</option>
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140 <option value="PuOr">PuOr: Purple - Orange</option>
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141 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
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142 <option value="RdGy">RdGy: Red - Gray</option>
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143 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
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144 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
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145 <option value="Spectral">Spectral</option>
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146 </param>
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147 </xml>
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148 <xml name="general_options">
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149 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
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150 <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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151 <param label="Track Padding" type="integer" value="20" name="trackPadding" help="Spacing between tracks in the genome view, in pixels." />
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152
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153 <param label="Enable Share Link" name="shareLink" type="boolean" checked="true" truevalue="true" falsevalue="false" />
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154 <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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155
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156 <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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157 <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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158 <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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159 <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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160
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161 <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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162 </section>
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163 </xml>
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164 <xml name="color_selection_minmax">
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165 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
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166 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
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167 auto case as well, but may be safe to just say "brewer colors? Pff,
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168 red/blue" -->
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169 <expand macro="auto_manual_tk"
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170 token_cond_label="Color"
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171 token_cond_name="color"
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172 token_select_label="Color Selection"
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173 token_select_name="color_select"
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174 token_automatic_label="Automatically selected"
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175 token_manual_label="Manual Color Selection">
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176 <expand macro="jb_color"
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177 label="JBrowse style.pos_color"
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178 name="style_pos_color"
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179 value="blue"
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180 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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181 <expand macro="jb_color"
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182 label="JBrowse style.neg_color"
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183 name="style_neg_color"
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184 value="red"
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185 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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186 </expand>
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187
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188 <conditional name="bicolor_pivot" label="Bicolor Pivot">
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189 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
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190 <option value="zero" selected="true">Zero</option>
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191 <option value="mean">Mean</option>
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192 <option value="custom">Custom Value</option>
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193 </param>
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194 <when value="zero" />
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195 <when value="mean" />
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196 <when value="custom">
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197 <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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198 </when>
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199 </conditional>
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200 </section>
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201 </xml>
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202
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203 <xml name="color_selection"
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204 token_scaling_lin_select="true"
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205 token_scaling_log_select="false"
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206 >
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207 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
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208 <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
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209 <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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210 <option value="score">Based on score</option>
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211 <option value="none" selected="true">Ignore score</option>
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212 </param>
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213 <when value="none">
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214 <!-- When no scaling is done, no scores available, then just let the
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215 user choose a base color for the track -->
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216 <expand macro="auto_color" />
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217 </when>
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218 <when value="score">
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219 <!-- Scaling -->
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220 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
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221 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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222 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option>
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223 <option value="logarithmic" selected="false">Logarithmic scaling</option>
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224 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
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225 </param>
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226
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227 <!-- Scaling Bounds -->
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228 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
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229 <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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230 <option value="automatic" selected="true">Automatically determined</option>
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231 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
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232 </param>
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233 <when value="automatic">
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234 </when>
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235 <when value="manual">
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236 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
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237 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
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238 </when>
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239 </conditional>
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240
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241 <!-- Scale color -->
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242 <conditional name="color_scheme" label="Color Scheme for scored features">
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243 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme">
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244 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
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245 <!--<option value="brewer">Brewer Color Schemes</option>-->
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246 </param>
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247 <when value="opacity">
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248 <!-- Single color selection mode -->
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249 <expand macro="auto_color" />
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250 </when>
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251 <!--<when value="brewer">-->
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252 <!--[> Brewer continuum selection <]-->
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253 <!--<expand macro="brewer_scheme" />-->
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254 <!--</when>-->
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255 </conditional>
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256 </when>
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257 </conditional>
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258 </section>
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259 </xml>
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260 <xml name="track_styling"
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261 token_classname="feature"
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262 token_label="product,name,id"
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263 token_description="note,description"
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264 token_height="10px"
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265 token_maxheight="600">
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266 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
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267 <param label="JBrowse style.className" type="text"
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268 name="style_classname"
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269 value="@CLASSNAME@"
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270 help="Set CSS style.className property"/>
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271 <param label="JBrowse style.label"
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272 type="text"
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273 name="style_label"
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274 value="@LABEL@"
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275 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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276 <param label="JBrowse style.description"
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277 type="text"
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278 name="style_description"
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279 value="@DESCRIPTION@"
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280 help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/>
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281 <param label="JBrowse style.height"
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282 type="text"
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283 name="style_height"
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284 value="@HEIGHT@"
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285 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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diff changeset
286 <param label="JBrowse maxHeight"
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diff changeset
287 type="text"
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288 name="max_height"
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289 value="@MAXHEIGHT@"
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290 help="Maximum height that the track is permitted to reach in pixels."/>
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291 </section>
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292 </xml>
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293
59
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294 <xml name="track_custom_config">
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295 <section name="jb_custom_config" title="JBrowse Custom Track Config [Advanced]" expanded="false">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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296 <repeat name="option" title="Custom Track Config Option">
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297 <param name="opt_key" type="text" label="Key for JBrowse track config option"
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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298 help="Multilevel keys (e.g., 'style.label') are delimited by a period character ('.').">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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299 <validator type="regex" message="Key must consist of alphanumeric characters only, possibly separated by the period character ('.')">^[\w]+(\.\w+)*$</validator>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff changeset
300 </param>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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301 <conditional name="opt_value">
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302 <param name="val_type" type="select" label="Choose the type of value for the option">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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303 <option value="text" selected="true">Text</option>
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304 <option value="integer">Integer number</option>
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305 <option value="float">Floating point number</option>
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306 <option value="boolean">Boolean</option>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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diff changeset
307 </param>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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308 <when value="text">
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309 <param name="val" type="text" label="Value for custom track option."
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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310 help="Will override other track options set elsewhere.">
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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311 <validator type="empty_field" />
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312 </param>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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313 </when>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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314 <when value="integer">
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315 <param name="val" type="integer" value="0" label="Value for custom track option."
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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316 help="Will override other track options set elsewhere." />
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317 </when>
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318 <when value="float">
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319 <param name="val" type="float" value="0" label="Value for custom track option."
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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320 help="Will override other track options set elsewhere." />
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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321 </when>
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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322 <when value="boolean">
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323 <param name="val" type="boolean" truevalue="true" falsevalue="false"
e29039f307c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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324 label="Value for custom track option."
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325 help="Will override other track options set elsewhere." />
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326 </when>
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327 </conditional>
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328 </repeat>
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329 </section>
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330 </xml>
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331
42
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332 <xml name="track_menu">
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333 <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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334 <repeat name="track_menu" title="Track Menu">
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diff changeset
335 <param label="Menu action"
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336 type="select"
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diff changeset
337 name="menu_action"
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338 help="Action performed when user clicks on the menu">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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339 <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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340 <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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341 <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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342 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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diff changeset
343 <param label="Menu label"
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diff changeset
344 type="text"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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345 name="menu_label"
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346 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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347 <expand macro="menu_sanitize" />
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348 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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diff changeset
349 <param label="Menu title"
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diff changeset
350 type="text"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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diff changeset
351 name="menu_title"
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352 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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diff changeset
353 <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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diff changeset
354 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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diff changeset
355 <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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diff changeset
356 type="text"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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diff changeset
357 name="menu_url"
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358 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
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diff changeset
359 <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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diff changeset
360 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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diff changeset
361 <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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diff changeset
362 type="select"
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
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diff changeset
363 name="menu_icon"
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diff changeset
364 help="Icon to display next to menu label">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
365 <option value="dijitIconBookmark" selected="true">Bookmark</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
366 <option value="dijitIconSave">Save</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
367 <option value="dijitIconPrint">Print</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
368 <option value="dijitIconCut">Cut</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
369 <option value="dijitIconCopy">Copy</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
370 <option value="dijitIconClear">Clear</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
371 <option value="dijitIconDelete">Delete</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
372 <option value="dijitIconUndo">Undo</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
373 <option value="dijitIconEdit">Edit</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
374 <option value="dijitIconNewTask">New Task</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
375 <option value="dijitIconEditTask">Edit Task</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
376 <option value="dijitIconEditProperty">Edit Property</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
377 <option value="dijitIconTask">Task</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
378 <option value="dijitIconFilter">Filter</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
379 <option value="dijitIconConfigure">Configure</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
380 <option value="dijitIconSearch">Search</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
381 <option value="dijitIconApplication">Application</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
382 <option value="dijitIconChart">Chart</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
383 <option value="dijitIconConnector">Connector</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
384 <option value="dijitIconDatabase">Database</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
385 <option value="dijitIconDocuments">Documents</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
386 <option value="dijitIconMail">Mail</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
387 <option value="dijitLeaf">Leaf</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
388 <option value="dijitIconFile">File</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
389 <option value="dijitIconFunction">Function</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
390 <option value="dijitIconKey">Key</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
391 <option value="dijitIconPackage">Package</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
392 <option value="dijitIconSample">Sample</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
393 <option value="dijitIconTable">Table</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
394 <option value="dijitIconUsers">Users</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
395 <option value="dijitIconFolderClosed">Folder Closed</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
396 <option value="dijitIconFolderOpen">Folder Open</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
397 <option value="dijitIconError">Error</option>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
398 </param>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
399 </repeat>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
400 </section>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
401 </xml>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
402
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
403 <xml name="menu_sanitize">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
404 <sanitizer>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
405 <valid>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
406 <add value="{"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
407 <add value="}"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
408 <add value="!"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
409 <add value="?"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
410 <add value="&amp;"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
411 <add value="+"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
412 <add value="="/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
413 <add value="'"/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
414 <add value='"'/>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
415 </valid>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
416 </sanitizer>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
417 </xml>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
418
16
318a0aa5075a Uploaded manually
iuc
parents: 13
diff changeset
419 <xml name="input_conditional" token_label="Track Data" token_format="data">
318a0aa5075a Uploaded manually
iuc
parents: 13
diff changeset
420 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
318a0aa5075a Uploaded manually
iuc
parents: 13
diff changeset
421 </xml>
42
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
422 <xml name="citations">
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
423 <citations>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
424 <citation type="doi">10.1101/gr.094607.109</citation>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
425 </citations>
c1451868f8d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0bfb0de98c918860c21808e8832caad9f0535975
iuc
parents: 40
diff changeset
426 </xml>
55
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
427
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
428 <xml name="canvas_options">
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
429 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
430 <param label="Transcript type"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
431 name="transcriptType"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
432 type="text"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
433 value=""
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
434 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
435 optional="True"/>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
436 <param label="Subfeatures type"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
437 name="subParts"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
438 type="text"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
439 value=""
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
440 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
441 optional="True"/>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
442 <param label="Implied UTRs"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
443 name="impliedUTRs"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
444 type="boolean"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
445 checked="false"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
446 truevalue="true"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
447 falsevalue="false"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
448 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"/>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
449 </section>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
450 </xml>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
451
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
452 <xml name="html_options">
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
453 <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false">
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
454 <param label="Top level features"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents: 54
diff changeset
455 name="topLevelFeatures"
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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456 type="text"
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457 help="Select which top level features should be displayed. If empty, will try to display all features. If your input files represents gene→mRNA→exon/CDS/UTR, you should use mRNA if exons don't render."
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61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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458 optional="True"/>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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459 </section>
61a47bf57b3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
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460 </xml>
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c77c1d5baadb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
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461 </macros>