Mercurial > repos > fubar > jbrowse2

annotate macros.xml @ 97:74074746ccd8 draft

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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
author fubar
date Sat, 01 Jun 2024 05:37:13 +0000
parents 4c517a0041a8
children b1260bca5fdc
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1 <macros>
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2 <token name="@TOOL_VERSION@">2.11.0</token>
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3 <xml name="edamInc">
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4 <edam_topics>
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5 <edam_topic>topic_3307</edam_topic>
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6 <edam_topic>topic_0092</edam_topic>
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7 </edam_topics>
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8 <edam_operations>
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9 <edam_operation>operation_0573</edam_operation>
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10 <edam_operation>operation_0564</edam_operation>
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11 </edam_operations>
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12 </xml>
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13 <xml name="requirements">
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14 <requirements>
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15 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement>
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16 <requirement type="package" version="1.81">biopython</requirement>
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17 <requirement type="package" version="0.7.1">bcbio-gff</requirement>
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18 <requirement type="package" version="1.19">samtools</requirement>
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19 <requirement type="package" version="6.0.1">pyyaml</requirement>
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20 <requirement type="package" version="1.11">tabix</requirement>
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21 <requirement type="package" version="4.6.0">findutils</requirement>
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22 <requirement type="package" version="0.0.12-0">hictk</requirement>
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23 <requirement type="package" version="3.0">zip</requirement>
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24 <yield/>
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25 </requirements>
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26 </xml>
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27 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
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28 <token name="@WRAPPER_VERSION@">galaxy2</token>
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29 <token name="@ATTRIBUTION@"><![CDATA[
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30 **Attribution**
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31 This Galaxy tool relies on the JBrowse2, maintained by the GMOD Community. The Galaxy wrapper is
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32 maintained by Ross Lazarus and Bjoern Gruening until the IUC complete their own.
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33 ]]>
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34 </token>
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35 <xml name="creators">
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36 <creator>
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37 <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena" />
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38 <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud" />
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39 <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/" />
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40 </creator>
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41 </xml>
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42 <xml name="genome_selector"
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43 token_help=""
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44 token_label="Fasta sequences"
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45 token_optional="False" >
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46 <conditional name="reference_genome">
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47 <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references">
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48 <option selected="True" value="indexed">Use a built-in genome</option>
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49 <option value="history">Use a genome from history</option>
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50 </param>
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51 <when value="indexed">
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52 <param name="genomes" type="select" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@">
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53 <options from_data_table="all_fasta">
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54 <filter column="2" type="sort_by"/>
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55 <validator message="No genomes are available for the selected input dataset" type="no_options"/>
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56 </options>
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57 </param>
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58 </when>
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59 <when value="history">
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60 <param name="genomes" type="data" format="fasta" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@" multiple="True"/>
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61 </when>
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62 </conditional>
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63 </xml>
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64 <xml name="auto_manual_tk" token_cond_label="Color" token_cond_name="color" token_select_label="Color Specification" token_select_name="color_select" token_automatic_label="Automatically selected" token_manual_label="Manual Color Selection">
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65 <conditional name="@COND_NAME@" label="@COND_LABEL@">
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66 <param name="@SELECT_NAME@" type="select" label="@SELECT_LABEL@">
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67 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
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68 <option value="manual">@MANUAL_LABEL@</option>
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69 </param>
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70 <when value="automatic">
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71 </when>
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72 <when value="manual">
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73 <yield/>
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74 </when>
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75 </conditional>
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76 </xml>
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77 <xml name="jb_color" token_label="JBrowse style.color" token_name="style_color" token_value="goldenrod" 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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78 <param name="@NAME@" type="color" value="@VALUE@" label="@LABEL@" help="@HELP@">
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79 <sanitizer>
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80 <valid initial="string.letters,string.digits">
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81 <add value="#"/>
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82 </valid>
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83 </sanitizer>
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84 </param>
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85 </xml>
97
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86 <xml name="auto_color" token_cond_label="Color" token_cond_name="color" token_select_label="Color Selection" token_select_name="color_select" token_automatic_label="Automatically selected" token_manual_label="Manual Color Selection">
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87 <expand macro="auto_manual_tk" cond_label="@COND_LABEL@" cond_name="@COND_NAME@" select_label="@SELECT_LABEL@" select_name="@SELECT_NAME@" automatic_label="@AUTOMATIC_LABEL@" manual_label="@MANUAL_LABEL@">
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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88 <expand macro="jb_color"/>
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89 <yield/>
0
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90 </expand>
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91 </xml>
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92 <xml name="brewer_scheme">
97
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93 <param name="brewer_scheme" type="select" label="Brewer color Scheme">
0
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94 <option value="BrBg">BrBg: Brown - Blue Green</option>
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95 <option value="PiYg">PiYg: Pink - Yellow Green</option>
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96 <option value="PRGn">PRGn: Purple Red - Green</option>
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97 <option value="PuOr">PuOr: Purple - Orange</option>
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98 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
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99 <option value="RdGy">RdGy: Red - Gray</option>
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100 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
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101 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
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102 <option value="Spectral">Spectral</option>
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103 </param>
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104 </xml>
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105 <xml name="general_options">
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106 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false">
46
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107 <conditional name="ucol">
97
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108 <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form" help="A collection of bam/vcf and other track types will be converted into a JBrowse2 automatically">
46
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109 <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option>
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110 <option value="collect">Convert a collection of suitable track files</option>
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111 </param>
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112 <when value="collect">
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113 <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/>
46
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114 </when>
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115 <when value="form">
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116 </when>
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117 </conditional>
97
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118 <param name="zipOut" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create a zip archive for downloading rather than viewing " help="Default is to make an interactive browser appear when the 'eye' icon is activated"/>
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119 <param name="defaultLocation" type="text" value="" label="Subset to display to new users" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678"/>
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120 <param name="session_name" type="text" value="New JB2 session" label="Session name" help="Displayed at the top of the window"/>
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121 <param name="enableAnalytics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166"/>
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122 <param name="primary_color" type="color" value="#0D233F" label="Primary color">
0
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123 <sanitizer>
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124 <valid initial="string.ascii_letters,string.digits">
97
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125 <add value="#"/>
0
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126 </valid>
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127 </sanitizer>
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128 </param>
97
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129 <param name="secondary_color" type="color" value="#721E63" label="Secondary color">
0
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130 <sanitizer>
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131 <valid initial="string.ascii_letters,string.digits">
97
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132 <add value="#"/>
0
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133 </valid>
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134 </sanitizer>
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135 </param>
97
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136 <param name="tertiary_color" type="color" value="#135560" label="Tertiary color">
0
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137 <sanitizer>
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138 <valid initial="string.ascii_letters,string.digits">
97
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139 <add value="#"/>
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140 </valid>
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141 </sanitizer>
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142 </param>
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143 <param name="quaternary_color" type="color" value="#FFB11D" label="Quaternary color">
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144 <sanitizer>
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145 <valid initial="string.ascii_letters,string.digits">
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146 <add value="#"/>
0
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147 </valid>
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148 </sanitizer>
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149 </param>
97
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150 <param name="font_size" type="integer" value="10" label="Font size"/>
0
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151 </section>
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152 </xml>
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153 <xml name="color_selection_minmax">
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154 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
97
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155 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
0
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156 auto case as well, but may be safe to just say "brewer colors? Pff,
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157 red/blue" -->
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158 <expand macro="auto_manual_tk" token_cond_label="Color" token_cond_name="color" token_select_label="Color Selection" token_select_name="color_select" token_automatic_label="Automatically selected" token_manual_label="Manual Color Selection">
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159 <expand macro="jb_color" label="JBrowse style.pos_color" name="style_pos_color" value="blue" 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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160 <expand macro="jb_color" label="JBrowse style.neg_color" name="style_neg_color" value="red" 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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161 </expand>
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162 <conditional name="bicolor_pivot" label="Bicolor Pivot">
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163 <param name="bicolor_pivot_select" type="select" label="Bicolor Pivot">
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164 <option value="zero" selected="true">Zero</option>
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165 <option value="mean">Mean</option>
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166 <option value="custom">Custom Value</option>
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167 </param>
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168 <when value="zero"/>
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169 <when value="mean"/>
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170 <when value="custom">
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171 <param name="pivot_point" type="float" value="0.0" label="JBrowse style.bicolor_pivot" help="Where to change from pos_color to neg_color when drawing bicolor plots."/>
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172 </when>
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173 </conditional>
0
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174 </section>
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175 </xml>
97
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176 <xml name="color_selection" token_scaling_lin_select="true" token_scaling_log_select="false">
0
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177 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
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178 <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
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179 <param name="color_score_select" type="select" label="Color Score Algorithm" 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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180 <option value="score">Based on score</option>
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181 <option value="none" selected="true">Ignore score</option>
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182 </param>
97
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183 <when value="none">
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184 <!-- When no scaling is done, no scores available, then just let the
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185 user choose a base color for the track -->
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186 <expand macro="auto_color"/>
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187 </when>
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188 <when value="score">
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189 <!-- Scaling -->
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190 <param name="score_scaling" type="select" label="JBrowse style.color function's score scaling" 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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191 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option>
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192 <option value="logarithmic" selected="false">Logarithmic scaling</option>
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193 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
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194 </param>
97
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195 <!-- Scaling Bounds -->
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196 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
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197 <param name="scale_select" type="select" label="How should minimum and maximum values be determined for the scores of the features">
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198 <option value="automatic" selected="true">Automatically determined</option>
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199 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
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200 </param>
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201 <when value="automatic"/>
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202 <when value="manual">
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203 <param name="minimum" type="integer" value="0" label="Minimum expected score"/>
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204 <param name="maximum" type="integer" value="100" label="Maximum expected score"/>
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205 </when>
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206 </conditional>
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207 <!-- Scale color -->
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208 <conditional name="color_scheme" label="Color Scheme for scored features">
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209 <param name="score_scheme" type="select" label="JBrowse style.color function's color scheme for scored values">
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210 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
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211 <!--<option value="brewer">Brewer Color Schemes</option>-->
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212 </param>
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213 <when value="opacity">
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214 <!-- Single color selection mode -->
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215 <expand macro="auto_color"/>
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216 </when>
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217 <!--<when value="brewer">-->
0
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218 <!--[> Brewer continuum selection <]-->
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219 <!--<expand macro="brewer_scheme" />-->
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220 <!--</when>-->
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221 </conditional>
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222 </when>
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223 </conditional>
0
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224 </section>
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225 </xml>
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226 <xml name="track_visibility">
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227 <param name="track_visibility" type="select" label="Track Visibility">
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228 <option value="default_off">Off when browser opens</option>
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229 <option value="default_on" selected="true">On when browser opens</option>
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230 </param>
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231 </xml>
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232 <xml name="track_styling_linear">
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233 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/>
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234 <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/>
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235 <param name="display_mode" type="select" label="Display mode">
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236 <option value="normal" selected="true">normal</option>
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237 <option value="compact">compact</option>
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238 <option value="reducedRepresentation">reducedRepresentation</option>
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239 <option value="collapse">collapse</option>
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240 </param>
97
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241 <param name="max_height" type="integer" value="600" label="Max height" help="Maximum height that the track is permitted to reach in pixels."/>
0
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242 </xml>
85
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243 <xml name="track_styling_vgp">
0
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244 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
97
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245 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/>
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246 <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/>
0
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247 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
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248 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option>
5
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249 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option>
0
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250 <option value="LinearArcDisplay">LinearArcDisplay</option>
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251 </param>
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252 </section>
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253 </xml>
97
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254 <xml name="track_styling_feature">
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255 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
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256 <conditional name="track_style">
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257 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
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258 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option>
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259 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option>
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260 <option value="LinearArcDisplay">LinearArcDisplay</option>
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261 </param>
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262 <when value="LinearPileupDisplay">
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263 <expand macro="track_styling_linear"/>
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264 </when>
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265 <when value="LinearBasicDisplay">
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266 <expand macro="track_styling_linear"/>
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267 <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729
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268 and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41 -->
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269 <param name="label" type="text" value="jexl:get(feature,'name') || get(feature,'id')" label="Features label" help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
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270 <sanitizer>
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271 <valid initial="default">
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272 <add value="|"/>
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273 <add value="{"/>
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274 <add value="}"/>
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275 <add value="!"/>
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276 <add value="?"/>
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277 <add value="+"/>
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278 <add value="="/>
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279 <add value="'"/>
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280 </valid>
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281 </sanitizer>
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282 </param>
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283 <param name="description" type="text" value="jexl:get(feature,'note') || get(feature,'description')" label="Features description" help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax">
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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284 <sanitizer>
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285 <valid initial="default">
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286 <add value="|"/>
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287 <add value="{"/>
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288 <add value="}"/>
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289 <add value="!"/>
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290 <add value="?"/>
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291 <add value="+"/>
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292 <add value="="/>
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293 <add value="'"/>
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294 </valid>
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295 </sanitizer>
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296 </param>
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297 </when>
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298 <when value="LinearArcDisplay"/>
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299 </conditional>
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300 </section>
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301 </xml>
0
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302 <xml name="track_styling_xam">
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303 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
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304 <conditional name="track_style">
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305 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
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306 <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option>
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307 <option value="LinearPileupDisplay">LinearPileupDisplay</option>
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308 <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option>
62
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309 <option value="LinearReadArcsDisplay">LinearReadArcsDisplay</option>
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310 <option value="LinearReadCloudDisplay">LinearReadCloudDisplay</option>
0
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311 </param>
62
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312 <!-- TODO check if possible to handle more options than just the display style-->
0
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313 <when value="LinearAlignmentsDisplay"/>
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314 <when value="LinearPileupDisplay"/>
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315 <when value="LinearSNPCoverageDisplay">
97
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316 <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/>
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317 <param name="minScore" type="integer" value="" optional="true" label="Min score"/>
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318 <param name="maxScore" type="integer" value="" optional="true" label="Max score"/>
0
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319 </when>
62
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320 <when value="LinearReadArcsDisplay"/>
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321 <when value="LinearReadCloudDisplay"/>
0
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322 </conditional>
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323 </section>
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324 </xml>
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325 <xml name="track_styling_vcf">
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326 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
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327 <conditional name="track_style">
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328 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
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329 <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option>
62
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330 <option value="LinearPairedArcDisplay">LinearPairedArcDisplay</option>
0
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331 </param>
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332 <when value="LinearVariantDisplay">
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333 <expand macro="track_styling_linear"/>
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334 </when>
62
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335 <when value="LinearPairedArcDisplay"/>
0
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336 </conditional>
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337 </section>
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338 </xml>
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339 <xml name="track_styling_bigwig">
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340 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
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341 <conditional name="track_style">
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342 <param name="display" type="select" label="Display style" help="How the track will be displayed by default">
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343 <option value="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option>
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344 </param>
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345 <when value="LinearWiggleDisplay">
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346 <param name="autoscale" type="select" label="Autoscale type">
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347 <option value="local" selected="true">Local</option>
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348 <option value="global">Global</option>
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349 <option value="globalsd">Global ± 3σ</option>
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350 <option value="localsd">Local ± 3σ</option>
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351 </param>
97
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352 <param name="resolution" type="integer" value="1" label="Resolution"/>
0
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353 <param name="summaryScoreMode" type="select" label="Autoscale type">
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354 <option value="max">Max</option>
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355 <option value="min">Min</option>
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356 <option value="avg">Avg</option>
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357 <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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358 </param>
97
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359 <param name="filled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Fill in histogram"/>
0
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360 <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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361 <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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362 <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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363 </param>
97
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364 <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/>
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365 <param name="minScore" type="integer" value="" optional="true" label="Min score"/>
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366 <param name="maxScore" type="integer" value="" optional="true" label="Max score"/>
0
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367 </when>
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368 </conditional>
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369 </section>
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370 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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371 <xml name="track_menu">
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372 <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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373 <repeat name="track_menu" title="Track Menu">
97
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374 <param name="menu_action" type="select" label="Menu action" help="Action performed when user clicks on the menu">
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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375 <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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376 <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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377 <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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378 </param>
97
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379 <param name="menu_label" type="text" label="Menu label" help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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380 <expand macro="menu_sanitize"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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381 </param>
97
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382 <param name="menu_title" type="text" label="Menu title" help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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383 <expand macro="menu_sanitize"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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384 </param>
97
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diff changeset
385 <param name="menu_url" type="text" label="Menu url" help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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386 <expand macro="menu_sanitize"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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387 </param>
97
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388 <param name="menu_icon" type="select" label="Menu icon" help="Icon to display next to menu label">
0
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389 <option value="dijitIconBookmark" selected="true">Bookmark</option>
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390 <option value="dijitIconSave">Save</option>
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391 <option value="dijitIconPrint">Print</option>
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392 <option value="dijitIconCut">Cut</option>
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393 <option value="dijitIconCopy">Copy</option>
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394 <option value="dijitIconClear">Clear</option>
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395 <option value="dijitIconDelete">Delete</option>
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396 <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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397 <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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398 <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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399 <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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400 <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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401 <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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402 <option value="dijitIconFilter">Filter</option>
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403 <option value="dijitIconConfigure">Configure</option>
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404 <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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405 <option value="dijitIconApplication">Application</option>
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406 <option value="dijitIconChart">Chart</option>
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407 <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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408 <option value="dijitIconDatabase">Database</option>
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409 <option value="dijitIconDocuments">Documents</option>
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410 <option value="dijitIconMail">Mail</option>
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411 <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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412 <option value="dijitIconFile">File</option>
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413 <option value="dijitIconFunction">Function</option>
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414 <option value="dijitIconKey">Key</option>
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415 <option value="dijitIconPackage">Package</option>
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416 <option value="dijitIconSample">Sample</option>
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417 <option value="dijitIconTable">Table</option>
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418 <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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419 <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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420 <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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421 <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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422 </param>
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423 </repeat>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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424 </section>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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425 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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426 <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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427 <sanitizer>
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diff changeset
428 <valid>
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 <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
430 <add value="}"/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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431 <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
432 <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
433 <add value="&amp;"/>
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 <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
435 <add value="="/>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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436 <add value="'"/>
97
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437 <add value="&quot;"/>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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438 </valid>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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439 </sanitizer>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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440 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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441 <xml name="input_conditional" token_label="Track Data" token_format="data">
46
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442 <conditional name="useuri">
97
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443 <param name="insource" type="select" label="Define track data as a history file or an internet URI" help="A public URI implies that all the associated tabix files are also in place. They are created for history files">
93
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444 <option value="history" selected="true">Track data from a history file</option>
97
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445 <option value="uri">Tabix data URI - index files must be available at corresponding URI</option>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
446 </param>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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447 <when value="history">
97
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448 <param name="annotation" type="data" format="@FORMAT@" optional="true" label="@LABEL@" multiple="True"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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449 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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450 <when value="uri">
97
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parents: 93
diff changeset
451 <param name="annouri" type="text" label="@LABEL@"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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452 <param name="annoname" type="text" label="Short name for track display">
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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453 <sanitizer invalid_char="_">
97
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parents: 93
diff changeset
454 <valid initial="string.printable">
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents: 93
diff changeset
455 <remove value="'"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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456 </valid>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
457 </sanitizer>
46
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diff changeset
458 </param>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 89
diff changeset
459 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
460 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 89
diff changeset
461 </xml>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 89
diff changeset
462 <xml name="pafref_conditional" token_label="Track Data" token_format="data">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
463 <conditional name="pafuseuri">
97
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diff changeset
464 <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place.">
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
465 <option value="history" selected="true">PAF reference comparison genome from a history file</option>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
466 <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents: 89
diff changeset
467 </param>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
468 <when value="history">
97
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diff changeset
469 <param name="annotation" type="data" format="@FORMAT@" label="@LABEL@" help="Add all PAF reference comparison genomes used to make the PAF" multiple="true"/>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
470 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
471 <when value="uri">
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
472 <repeat name="refuri" title="PAF reference comparison genome URI" min="1">
97
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diff changeset
473 <param name="annotation" type="text" label="@LABEL@"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff changeset
474 <param name="annoname" type="text" label="Short name for this reference" help="Short names take less track space">
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff changeset
475 <sanitizer invalid_char="_">
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff changeset
476 <valid initial="string.printable">
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff changeset
477 <remove value="'"/>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff changeset
478 </valid>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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479 </sanitizer>
93
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
480 </param>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
481 </repeat>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
482 </when>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
483 </conditional>
4c517a0041a8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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diff changeset
484 </xml>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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485 <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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486 <citations>
97
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487 <citation type="doi">10.1186/s13059-016-0924-1</citation>
74074746ccd8 planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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488 <citation type="doi">10.1101/gr.094607.109</citation>
0
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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489 </citations>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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490 </xml>
d78175596286 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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491 </macros>