annotate macros.xml @ 3:7342f467507b draft

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author iuc
date Thu, 31 Dec 2015 13:58:43 -0500
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1 <?xml version="1.0"?>
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2 <macros>
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3 <xml name="requirements">
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4 <requirements>
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5 <requirement type="package" version="1.12.0">jbrowse</requirement>
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6 <requirement type="package" version="1.12.0">bundle_jbrowse</requirement>
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7 <requirement type="package" version="2.7">python</requirement>
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8 <requirement type="package" version="5.18.1">perl</requirement>
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9 <requirement type="package" version="1.66">biopython</requirement>
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10 <requirement type="package" version="0.6.2">bcbiogff</requirement>
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11 <requirement type="package" version="1.2">samtools</requirement>
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12 <requirement type="package" version="3.11">pyyaml</requirement>
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13 <yield/>
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14 </requirements>
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15 </xml>
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16 <token name="@WRAPPER_VERSION@">1.0</token>
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17 <xml name="stdio">
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18 <stdio>
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19 <exit_code range="1:"/>
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20 <exit_code range=":-1"/>
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21 <regex match="Error:"/>
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22 <regex match="Exception:"/>
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23 </stdio>
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24 </xml>
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25 <token name="@ATTRIBUTION@"><![CDATA[
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26 **Attribution**
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27
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28 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
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29 ]]>
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30 </token>
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31 <xml name="auto_manual_tk"
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32 token_cond_label="Color"
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33 token_cond_name="color"
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34 token_select_label="Color Specification"
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35 token_select_name="color_select"
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36 token_automatic_label="Automatically selected"
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37 token_manual_label="Manual Color Selection">
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38 <conditional name="@COND_NAME@" label="@COND_LABEL@">
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39 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@">
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40 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option>
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41 <option value="manual">@MANUAL_LABEL@</option>
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42 </param>
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43 <when value="automatic">
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44 </when>
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45 <when value="manual">
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46 <yield />
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47 </when>
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48 </conditional>
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49 </xml>
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50
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51 <xml name="jb_color"
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52 token_label="JBrowse style.color"
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53 token_name="style_color"
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54 token_value="goldenrod"
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55 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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56 >
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57 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
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58 <sanitizer>
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59 <valid initial="string.letters,string.digits">
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60 <add value="#" />
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61 </valid>
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62 </sanitizer>
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63 </param>
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64 </xml>
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65
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66 <xml name="auto_color"
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67 token_cond_label="Color"
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68 token_cond_name="color"
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69 token_select_label="Color Selection"
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70 token_select_name="color_select"
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71 token_automatic_label="Automatically selected"
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72 token_manual_label="Manual Color Selection">
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73 <expand macro="auto_manual_tk"
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74 cond_label="@COND_LABEL@"
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75 cond_name="@COND_NAME@"
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76 select_label="@SELECT_LABEL@"
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77 select_name="@SELECT_NAME@"
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78 automatic_label="@AUTOMATIC_LABEL@"
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79 manual_label="@MANUAL_LABEL@">
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80 <expand macro="jb_color" />
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81 <yield />
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82 </expand>
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83 </xml>
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84
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85
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86
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87 <xml name="brewer_scheme">
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88 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
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89 <option value="BrBg">BrBg: Brown - Blue Green</option>
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90 <option value="PiYg">PiYg: Pink - Yellow Green</option>
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91 <option value="PRGn">PRGn: Purple Red - Green</option>
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92 <option value="PuOr">PuOr: Purple - Orange</option>
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93 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
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94 <option value="RdGy">RdGy: Red - Gray</option>
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95 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
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96 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
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97 <option value="Spectral">Spectral</option>
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98 </param>
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99 </xml>
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100 <xml name="color_selection_minmax">
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101 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
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102 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
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103 auto case as well, but may be safe to just say "brewer colors? Pff,
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104 red/blue" -->
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105 <expand macro="auto_manual_tk"
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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="jb_color"
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113 label="JBrowse style.pos_color"
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114 name="style_pos_color"
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115 value="blue"
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116 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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117 <expand macro="jb_color"
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118 label="JBrowse style.neg_color"
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119 name="style_neg_color"
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120 value="red"
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121 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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122 </expand>
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123
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124 <conditional name="bicolor_pivot" label="Bicolor Pivot">
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125 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
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126 <option value="zero" selected="true">Zero</option>
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127 <option value="mean">Mean</option>
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128 <option value="custom">Custom Value</option>
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129 </param>
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130 <when value="zero" />
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131 <when value="mean" />
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132 <when value="custom">
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133 <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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134 </when>
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135 </conditional>
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136 </section>
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137 </xml>
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138
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139 <xml name="color_selection"
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140 token_scaling_lin_select="true"
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141 token_scaling_log_select="false"
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142 >
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143 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
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144 <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
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145 <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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146 <option value="score">Based on score</option>
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147 <option value="none" selected="true">Ignore score</option>
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148 </param>
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149 <when value="none">
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150 <!-- When no scaling is done, no scores available, then just let the
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151 user choose a base color for the track -->
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152 <expand macro="auto_color" />
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153 </when>
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154 <when value="score">
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155 <!-- Scaling -->
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156 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
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157 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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158 <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
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159 <option value="logarithmic" selected="" >Logarithmic scaling</option>
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160 <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
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161 </param>
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162
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163 <!-- Scaling Bounds -->
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164 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
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165 <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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166 <option value="automatic" selected="true">Automatically determined</option>
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167 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
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168 </param>
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169 <when value="automatic">
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170 </when>
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171 <when value="manual">
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172 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
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173 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
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174 </when>
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175 </conditional>
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176
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177 <!-- Scale color -->
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178 <conditional name="color_scheme" label="Color Scheme for scored features">
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179 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme">
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180 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
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181 <!--<option value="brewer">Brewer Color Schemes</option>-->
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182 </param>
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183 <when value="opacity">
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184 <!-- Single color selection mode -->
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185 <expand macro="auto_color" />
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186 </when>
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187 <!--<when value="brewer">-->
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188 <!--[> Brewer continuum selection <]-->
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189 <!--<expand macro="brewer_scheme" />-->
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190 <!--</when>-->
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191 </conditional>
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192 </when>
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193 </conditional>
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194 </section>
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195 </xml>
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196 <xml name="track_styling"
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197 token_classname="feature"
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198 token_label="name,id"
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199 token_description="note,description"
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200 token_height="100px">
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201 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
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202 <param label="JBrowse style.className" type="text"
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203 name="style_classname"
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204 value="@CLASSNAME@"
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205 help="Set CSS style.className property"/>
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206 <param label="JBrowse style.label"
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207 type="text"
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208 name="style_label"
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209 value="@LABEL@"
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210 help="Comma-separated list of case-insensitive feature tags to use for showing the feature's label. The first one found will be used. Default 'name,id'" />
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211 <param label="JBrowse style.description"
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212 type="text"
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213 name="style_description"
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214 value="@DESCRIPTION@"
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215 help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/>
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216 <param label="JBrowse style.height"
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217 type="text"
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218 name="style_height"
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219 value="@HEIGHT@"
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220 help="Height in pixels of glyphs. Default value varies from glyph to glyph. Note that the 'compact' displayMode uses style->height * 0.35 so changing style height can adjust the compact visualization."/>
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221 </section>
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222 </xml>
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223
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224 <xml name="input_conditional" token_label="Track Data" token_format="data">
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225 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
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226 </xml>
0
2c9e5136b416 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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227 </macros>