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annotate macros.xml @ 0:d78175596286 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
author fubar
date Mon, 08 Jan 2024 09:20:33 +0000
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children 2de9f585505b
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d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@TOOL_VERSION@">2.10.0</token>
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4 <xml name = "edamInc">
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5 <edam_topics>
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6 <edam_topic>topic_3307</edam_topic>
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7 <edam_topic>topic_0092</edam_topic>
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8 </edam_topics>
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9 <edam_operations>
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10 <edam_operation>operation_0573</edam_operation>
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11 <edam_operation>operation_0564</edam_operation>
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12 </edam_operations>
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13 </xml>
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14 <xml name="requirements">
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15 <requirements>
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16 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
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17 <requirement type="package" version="1.82">biopython</requirement>
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18 <requirement type="package" version="0.7.0">bcbio-gff</requirement>
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19 <requirement type="package" version="1.19">samtools</requirement>
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20 <requirement type="package" version="6.0.1">pyyaml</requirement>
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21 <requirement type="package" version="1.11">tabix</requirement>
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22 <requirement type="package" version="4.6.0">findutils</requirement>
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23 <yield/>
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24 </requirements>
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25 </xml>
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26 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
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27 <token name="@WRAPPER_VERSION@">galaxy0</token>
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28 <token name="@ATTRIBUTION@"><![CDATA[
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29 **Attribution**
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30 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by the IUC
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31 This xml currently fails silently when profile=22.05 is set.
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32 ]]>
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33 </token>
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34 <xml name="genome_selector"
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35 token_help=""
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36 token_label="Fasta sequences"
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37 token_optional="False" >
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38 <conditional name="reference_genome">
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39 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
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40 <option selected="True" value="indexed">Use a built-in genome</option>
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41 <option value="history">Use a genome from history</option>
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42 </param>
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43 <when value="indexed">
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44 <param
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45 help="@HELP@"
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46 label="@LABEL@"
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47 name="genomes"
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48 type="select"
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49 optional="@OPTIONAL@"
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50 >
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51 <options from_data_table="all_fasta">
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52 <filter column="2" type="sort_by" />
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53 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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54 </options>
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55 </param>
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56 </when>
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57 <when value="history">
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58 <param
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59 format="fasta"
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60 label="@LABEL@"
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61 help="@HELP@"
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62 name="genomes"
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63 type="data"
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64 optional="@OPTIONAL@"
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65 multiple="True" />
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66 </when>
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67 </conditional>
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68 </xml>
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69
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70 <xml name="auto_manual_tk"
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71 token_cond_label="Color"
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72 token_cond_name="color"
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73 token_select_label="Color Specification"
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74 token_select_name="color_select"
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75 token_automatic_label="Automatically selected"
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76 token_manual_label="Manual Color Selection">
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77 <conditional name="@COND_NAME@" label="@COND_LABEL@">
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78 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
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79 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
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80 <option value="manual">@MANUAL_LABEL@</option>
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81 </param>
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82 <when value="automatic">
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83 </when>
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84 <when value="manual">
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85 <yield />
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86 </when>
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87 </conditional>
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88 </xml>
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89
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90 <xml name="jb_color"
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91 token_label="JBrowse style.color"
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92 token_name="style_color"
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93 token_value="goldenrod"
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94 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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95 >
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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96 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
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97 <sanitizer>
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98 <valid initial="string.letters,string.digits">
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99 <add value="#" />
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100 </valid>
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101 </sanitizer>
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102 </param>
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103 </xml>
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104
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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105 <xml name="auto_color"
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106 token_cond_label="Color"
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107 token_cond_name="color"
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108 token_select_label="Color Selection"
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109 token_select_name="color_select"
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110 token_automatic_label="Automatically selected"
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111 token_manual_label="Manual Color Selection">
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112 <expand macro="auto_manual_tk"
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113 cond_label="@COND_LABEL@"
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114 cond_name="@COND_NAME@"
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115 select_label="@SELECT_LABEL@"
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116 select_name="@SELECT_NAME@"
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117 automatic_label="@AUTOMATIC_LABEL@"
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118 manual_label="@MANUAL_LABEL@">
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119 <expand macro="jb_color" />
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120 <yield />
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121 </expand>
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122 </xml>
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123
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124
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125
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126 <xml name="brewer_scheme">
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127 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
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128 <option value="BrBg">BrBg: Brown - Blue Green</option>
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129 <option value="PiYg">PiYg: Pink - Yellow Green</option>
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130 <option value="PRGn">PRGn: Purple Red - Green</option>
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131 <option value="PuOr">PuOr: Purple - Orange</option>
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132 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
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133 <option value="RdGy">RdGy: Red - Gray</option>
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134 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
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135 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
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136 <option value="Spectral">Spectral</option>
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137 </param>
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138 </xml>
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139
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140 <xml name="general_options">
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141 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
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142 <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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143 <param label="Session name" type="text" name="session_name" value="New session" help="Displayed at the top of the window"/>
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144 <param label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166" name="enableAnalytics" type="boolean" checked="false" truevalue="true" falsevalue="false" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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145
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146 <param name="primary_color" type="color" label="Primary color" value="#0D233F">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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147 <sanitizer>
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148 <valid initial="string.ascii_letters,string.digits">
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149 <add value="#" />
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150 </valid>
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151 </sanitizer>
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152 </param>
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153 <param name="secondary_color" type="color" label="Secondary color" value="#721E63">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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154 <sanitizer>
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155 <valid initial="string.ascii_letters,string.digits">
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156 <add value="#" />
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157 </valid>
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158 </sanitizer>
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159 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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160 <param name="tertiary_color" type="color" label="Tertiary color" value="#135560">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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161 <sanitizer>
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162 <valid initial="string.ascii_letters,string.digits">
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163 <add value="#" />
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164 </valid>
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165 </sanitizer>
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166 </param>
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167 <param name="quaternary_color" type="color" label="Quaternary color" value="#FFB11D">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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168 <sanitizer>
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169 <valid initial="string.ascii_letters,string.digits">
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170 <add value="#" />
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171 </valid>
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172 </sanitizer>
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173 </param>
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174
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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175 <param label="Font size" name="font_size" type="integer" value="10" />
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176 </section>
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177 </xml>
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178
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179 <xml name="color_selection_minmax">
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180 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
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181 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
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182 auto case as well, but may be safe to just say "brewer colors? Pff,
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183 red/blue" -->
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184 <expand macro="auto_manual_tk"
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185 token_cond_label="Color"
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186 token_cond_name="color"
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187 token_select_label="Color Selection"
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188 token_select_name="color_select"
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189 token_automatic_label="Automatically selected"
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190 token_manual_label="Manual Color Selection">
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191 <expand macro="jb_color"
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192 label="JBrowse style.pos_color"
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193 name="style_pos_color"
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194 value="blue"
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195 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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196 <expand macro="jb_color"
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197 label="JBrowse style.neg_color"
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198 name="style_neg_color"
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199 value="red"
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200 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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201 </expand>
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202
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203 <conditional name="bicolor_pivot" label="Bicolor Pivot">
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204 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
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205 <option value="zero" selected="true">Zero</option>
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206 <option value="mean">Mean</option>
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207 <option value="custom">Custom Value</option>
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208 </param>
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209 <when value="zero" />
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210 <when value="mean" />
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211 <when value="custom">
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212 <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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213 </when>
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214 </conditional>
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215 </section>
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216 </xml>
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217
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218 <xml name="color_selection"
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219 token_scaling_lin_select="true"
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220 token_scaling_log_select="false"
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221 >
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222 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
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223 <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
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224 <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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225 <option value="score">Based on score</option>
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226 <option value="none" selected="true">Ignore score</option>
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227 </param>
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228 <when value="none">
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229 <!-- When no scaling is done, no scores available, then just let the
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230 user choose a base color for the track -->
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231 <expand macro="auto_color" />
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232 </when>
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233 <when value="score">
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234 <!-- Scaling -->
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235 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
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236 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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237 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option>
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238 <option value="logarithmic" selected="false">Logarithmic scaling</option>
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239 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
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240 </param>
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241
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242 <!-- Scaling Bounds -->
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243 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
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244 <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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245 <option value="automatic" selected="true">Automatically determined</option>
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246 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
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247 </param>
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248 <when value="automatic" />
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249 <when value="manual">
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250 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
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251 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
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252 </when>
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253 </conditional>
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254
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255 <!-- Scale color -->
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256 <conditional name="color_scheme" label="Color Scheme for scored features">
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257 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme">
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258 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
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259 <!--<option value="brewer">Brewer Color Schemes</option>-->
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260 </param>
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261 <when value="opacity">
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262 <!-- Single color selection mode -->
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263 <expand macro="auto_color" />
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264 </when>
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265 <!--<when value="brewer">-->
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266 <!--[> Brewer continuum selection <]-->
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267 <!--<expand macro="brewer_scheme" />-->
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268 <!--</when>-->
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269 </conditional>
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270 </when>
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271 </conditional>
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272 </section>
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273 </xml>
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274
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275 <xml name="track_visibility">
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276 <param type="select" label="Track Visibility" name="track_visibility">
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277 <option value="default_off">Off when browser opens</option>
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278 <option value="default_on" selected="true">On when browser opens</option>
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279 </param>
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280 </xml>
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281
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282 <xml name="track_styling_linear">
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283 <param label="Show labels" name="show_labels" type="boolean" checked="true" truevalue="true" falsevalue="false" />
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284 <param label="Show descriptions" name="show_descriptions" type="boolean" checked="true" truevalue="true" falsevalue="false" />
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285 <param name="display_mode" type="select" label="Display mode">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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286 <option value="normal" selected="true">normal</option>
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287 <option value="compact">compact</option>
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288 <option value="reducedRepresentation">reducedRepresentation</option>
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289 <option value="collapse">collapse</option>
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290 </param>
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291 <param label="Max height" name="max_height" type="integer" value="600" help="Maximum height that the track is permitted to reach in pixels."/>
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292 </xml>
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293
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294 <xml name="track_styling_feature">
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295 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
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296 <conditional name="track_style">
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297 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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298 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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299 <option value="LinearArcDisplay">LinearArcDisplay</option>
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300 </param>
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301 <when value="LinearBasicDisplay">
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302 <expand macro="track_styling_linear"/>
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303
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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304 <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729
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305 and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41 -->
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306 <param label="Features label"
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307 type="text"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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308 name="label"
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309 value="jexl:get(feature,'name') || get(feature,'id')"
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310 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
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311 <sanitizer>
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312 <valid initial="default">
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313 <add value="|" />
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314 <add value="{"/>
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315 <add value="}"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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316 <add value="!"/>
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317 <add value="?"/>
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318 <add value="+"/>
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319 <add value="="/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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320 <add value="'"/>
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321 </valid>
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322 </sanitizer>
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323 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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324 <param label="Features description"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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325 type="text"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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326 name="description"
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327 value="jexl:get(feature,'note') || get(feature,'description')"
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328 help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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329 <sanitizer>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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330 <valid initial="default">
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331 <add value="|" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
332 <add value="{"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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333 <add value="}"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
334 <add value="!"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
335 <add value="?"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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336 <add value="+"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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337 <add value="="/>
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338 <add value="'"/>
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339 </valid>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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340 </sanitizer>
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341 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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342 </when>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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343 <when value="LinearArcDisplay"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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344 </conditional>
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345 </section>
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346 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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347
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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348 <xml name="track_styling_xam">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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349 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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350 <conditional name="track_style">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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351 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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352 <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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353 <option value="LinearPileupDisplay">LinearPileupDisplay</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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354 <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
355 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
356 <when value="LinearAlignmentsDisplay"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
357 <when value="LinearPileupDisplay"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
358 <when value="LinearSNPCoverageDisplay">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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359 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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360 <param name="minScore" label="Min score" type="integer" value="" optional="true"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
361 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
362 </when>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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363 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
364 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
365 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
366
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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367 <xml name="track_styling_vcf">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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368 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
369 <conditional name="track_style">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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370 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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371 <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
372 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
373 <when value="LinearVariantDisplay">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
374 <expand macro="track_styling_linear"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
375 </when>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
376 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
377 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
378 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
379
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
380 <xml name="track_styling_bigwig">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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381 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
382 <conditional name="track_style">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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383 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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384 <option value="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
385 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
386 <when value="LinearWiggleDisplay">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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387 <param name="autoscale" type="select" label="Autoscale type">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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388 <option value="local" selected="true">Local</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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389 <option value="global">Global</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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390 <option value="globalsd">Global ± 3σ</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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391 <option value="localsd">Local ± 3σ</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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392 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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393 <param name="resolution" label="Resolution" type="integer" value="1"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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394 <param name="summaryScoreMode" type="select" label="Autoscale type">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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395 <option value="max">Max</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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396 <option value="min">Min</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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397 <option value="avg">Avg</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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398 <option value="whiskers" selected="true">Whiskers (combines all three)</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
399 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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400 <param name="filled" label="Fill in histogram" type="boolean" checked="true" truevalue="true" falsevalue="false" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
401 <param name="scaleType" type="select" label="Autoscale type">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
402 <option value="linear" selected="true">Linear</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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403 <option value="log">Log</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
404 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
405 <param name="displayCrossHatches" label="Draw cross hatches" type="boolean" checked="true" truevalue="true" falsevalue="false" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
406 <param name="minScore" label="Min score" type="integer" value="" optional="true"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
407 <param name="maxScore" label="Max score" type="integer" value="" optional="true"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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408 </when>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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409 </conditional>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
410 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
411 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
412
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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413 <xml name="track_menu">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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414 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
415 <repeat name="track_menu" title="Track Menu">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
416 <param label="Menu action"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
417 type="select"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
418 name="menu_action"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
419 help="Action performed when user clicks on the menu">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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420 <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>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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421 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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422 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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423 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
424 <param label="Menu label"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
425 type="text"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
426 name="menu_label"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
427 help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
428 <expand macro="menu_sanitize" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
429 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
430 <param label="Menu title"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
431 type="text"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
432 name="menu_title"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
433 help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
434 <expand macro="menu_sanitize" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
435 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
436 <param label="Menu url"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
437 type="text"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
438 name="menu_url"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
439 help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
440 <expand macro="menu_sanitize" />
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
441 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
442 <param label="Menu icon"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
443 type="select"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
444 name="menu_icon"
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
445 help="Icon to display next to menu label">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
446 <option value="dijitIconBookmark" selected="true">Bookmark</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
447 <option value="dijitIconSave">Save</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
448 <option value="dijitIconPrint">Print</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
449 <option value="dijitIconCut">Cut</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
450 <option value="dijitIconCopy">Copy</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
451 <option value="dijitIconClear">Clear</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
452 <option value="dijitIconDelete">Delete</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
453 <option value="dijitIconUndo">Undo</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
454 <option value="dijitIconEdit">Edit</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
455 <option value="dijitIconNewTask">New Task</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
456 <option value="dijitIconEditTask">Edit Task</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
457 <option value="dijitIconEditProperty">Edit Property</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
458 <option value="dijitIconTask">Task</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
459 <option value="dijitIconFilter">Filter</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
460 <option value="dijitIconConfigure">Configure</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
461 <option value="dijitIconSearch">Search</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
462 <option value="dijitIconApplication">Application</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
463 <option value="dijitIconChart">Chart</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
464 <option value="dijitIconConnector">Connector</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
465 <option value="dijitIconDatabase">Database</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
466 <option value="dijitIconDocuments">Documents</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
467 <option value="dijitIconMail">Mail</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
468 <option value="dijitLeaf">Leaf</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
469 <option value="dijitIconFile">File</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
470 <option value="dijitIconFunction">Function</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
471 <option value="dijitIconKey">Key</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
472 <option value="dijitIconPackage">Package</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
473 <option value="dijitIconSample">Sample</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
474 <option value="dijitIconTable">Table</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
475 <option value="dijitIconUsers">Users</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
476 <option value="dijitIconFolderClosed">Folder Closed</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
477 <option value="dijitIconFolderOpen">Folder Open</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
478 <option value="dijitIconError">Error</option>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
479 </param>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
480 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
481 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
482 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
483
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
484 <xml name="menu_sanitize">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
485 <sanitizer>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
486 <valid>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
487 <add value="{"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
488 <add value="}"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
489 <add value="!"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
490 <add value="?"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
491 <add value="&amp;"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
492 <add value="+"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
493 <add value="="/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
494 <add value="'"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
495 <add value='"'/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
496 </valid>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
497 </sanitizer>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
498 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
499
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff changeset
500
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
501 <xml name="input_conditional" token_label="Track Data" token_format="data">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
502 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
503 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff changeset
504 <xml name="citations">
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
505 <citations>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
506 <citation type="doi">10.1101/gr.094607.109</citation>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
507 </citations>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff changeset
508 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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509 </macros>