Mercurial > repos > iuc > jbrowse
annotate macros.xml @ 5:ae9382cfb6ac draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
author | iuc |
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date | Sat, 25 Jun 2016 15:06:43 -0400 |
parents | 7342f467507b |
children | ecbdfc775b9a |
rev | line source |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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1 <?xml version="1.0"?> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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2 <macros> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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3 <xml name="requirements"> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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4 <requirements> |
3 | 5 <requirement type="package" version="1.12.0">jbrowse</requirement> |
6 <requirement type="package" version="1.12.0">bundle_jbrowse</requirement> | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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7 <requirement type="package" version="2.7">python</requirement> |
3 | 8 <requirement type="package" version="5.18.1">perl</requirement> |
9 <requirement type="package" version="1.66">biopython</requirement> | |
10 <requirement type="package" version="0.6.2">bcbiogff</requirement> | |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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11 <requirement type="package" version="1.2">samtools</requirement> |
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b6a0e126dbee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a9cedb0983cc262cfdac04464566fdded884318b
iuc
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12 <requirement type="package" version="3.11">pyyaml</requirement> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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13 <yield/> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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14 </requirements> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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15 </xml> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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16 <token name="@WRAPPER_VERSION@">1.0</token> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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17 <xml name="stdio"> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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18 <stdio> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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19 <exit_code range="1:"/> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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20 <exit_code range=":-1"/> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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diff
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21 <regex match="Error:"/> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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22 <regex match="Exception:"/> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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23 </stdio> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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24 </xml> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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25 <token name="@ATTRIBUTION@"><![CDATA[ |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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26 **Attribution** |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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27 |
3 | 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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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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29 ]]> |
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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30 </token> |
3 | 31 <xml name="auto_manual_tk" |
32 token_cond_label="Color" | |
33 token_cond_name="color" | |
34 token_select_label="Color Specification" | |
35 token_select_name="color_select" | |
36 token_automatic_label="Automatically selected" | |
37 token_manual_label="Manual Color Selection"> | |
38 <conditional name="@COND_NAME@" label="@COND_LABEL@"> | |
39 <param type="select" label="@SELECT_LABEL@" name="@SELECT_NAME@"> | |
40 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option> | |
41 <option value="manual">@MANUAL_LABEL@</option> | |
42 </param> | |
43 <when value="automatic"> | |
44 </when> | |
45 <when value="manual"> | |
46 <yield /> | |
47 </when> | |
48 </conditional> | |
49 </xml> | |
50 | |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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51 <xml name="track_display"> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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52 <param type="select" label="Track Visibility" name="track_visibility"> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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53 <option value="default_off">Off for new users</option> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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54 <option value="default_on">On for new users</option> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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55 <option value="force">Force On</option> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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56 <option value="always">Always On (ignores URL parameters)</option> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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57 </param> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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58 </xml> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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59 |
3 | 60 <xml name="jb_color" |
61 token_label="JBrowse style.color" | |
62 token_name="style_color" | |
63 token_value="goldenrod" | |
64 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" | |
65 > | |
66 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@"> | |
67 <sanitizer> | |
68 <valid initial="string.letters,string.digits"> | |
69 <add value="#" /> | |
70 </valid> | |
71 </sanitizer> | |
72 </param> | |
73 </xml> | |
74 | |
75 <xml name="auto_color" | |
76 token_cond_label="Color" | |
77 token_cond_name="color" | |
78 token_select_label="Color Selection" | |
79 token_select_name="color_select" | |
80 token_automatic_label="Automatically selected" | |
81 token_manual_label="Manual Color Selection"> | |
82 <expand macro="auto_manual_tk" | |
83 cond_label="@COND_LABEL@" | |
84 cond_name="@COND_NAME@" | |
85 select_label="@SELECT_LABEL@" | |
86 select_name="@SELECT_NAME@" | |
87 automatic_label="@AUTOMATIC_LABEL@" | |
88 manual_label="@MANUAL_LABEL@"> | |
89 <expand macro="jb_color" /> | |
90 <yield /> | |
91 </expand> | |
92 </xml> | |
93 | |
94 | |
95 | |
96 <xml name="brewer_scheme"> | |
97 <param type="select" label="Brewer color Scheme" name="brewer_scheme"> | |
98 <option value="BrBg">BrBg: Brown - Blue Green</option> | |
99 <option value="PiYg">PiYg: Pink - Yellow Green</option> | |
100 <option value="PRGn">PRGn: Purple Red - Green</option> | |
101 <option value="PuOr">PuOr: Purple - Orange</option> | |
102 <option value="RdBu" selected="true">RdBu: Red - Blue</option> | |
103 <option value="RdGy">RdGy: Red - Gray</option> | |
104 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option> | |
105 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option> | |
106 <option value="Spectral">Spectral</option> | |
107 </param> | |
108 </xml> | |
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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109 <xml name="general_options"> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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110 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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111 <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'"/> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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112 <param label="Track Padding" type="integer" value="20" name="trackPadding" help="Spacing between tracks in the genome view, in pixels." /> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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113 |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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114 <param label="Enable Share Link" name="shareLink" type="boolean" checked="true" truevalue="true" falsevalue="false" /> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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115 <param label="About the Browser" type="text" name="aboutDescription" value="" help="Description of the browser to be used in the 'About' popup" /> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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116 |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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117 <param label="Show Track List" name="show_tracklist" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the track list"/> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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118 <param label="Show Navigation" name="show_nav" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the navigation menu"/> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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119 <param label="Show Overview" name="show_overview" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the overview bar"/> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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120 <param label="Show Menu" name="show_menu" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the menu bar"/> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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121 |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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122 <param label="Hide Genome Options" name="hideGenomeOptions" type="boolean" truevalue="true" falsevalue="false" help="Hide options for opening a sequence file"/> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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123 </section> |
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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124 </xml> |
3 | 125 <xml name="color_selection_minmax"> |
126 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false"> | |
127 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the | |
128 auto case as well, but may be safe to just say "brewer colors? Pff, | |
129 red/blue" --> | |
130 <expand macro="auto_manual_tk" | |
131 token_cond_label="Color" | |
132 token_cond_name="color" | |
133 token_select_label="Color Selection" | |
134 token_select_name="color_select" | |
135 token_automatic_label="Automatically selected" | |
136 token_manual_label="Manual Color Selection"> | |
137 <expand macro="jb_color" | |
138 label="JBrowse style.pos_color" | |
139 name="style_pos_color" | |
140 value="blue" | |
141 help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." /> | |
142 <expand macro="jb_color" | |
143 label="JBrowse style.neg_color" | |
144 name="style_neg_color" | |
145 value="red" | |
146 help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." /> | |
147 </expand> | |
148 | |
149 <conditional name="bicolor_pivot" label="Bicolor Pivot"> | |
150 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select"> | |
151 <option value="zero" selected="true">Zero</option> | |
152 <option value="mean">Mean</option> | |
153 <option value="custom">Custom Value</option> | |
154 </param> | |
155 <when value="zero" /> | |
156 <when value="mean" /> | |
157 <when value="custom"> | |
158 <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." /> | |
159 </when> | |
160 </conditional> | |
161 </section> | |
162 </xml> | |
163 | |
164 <xml name="color_selection" | |
165 token_scaling_lin_select="true" | |
166 token_scaling_log_select="false" | |
167 > | |
168 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling & Coloring Options [Advanced]" expanded="false"> | |
169 <conditional name="color_score" label="JBrowse style.color & Score relationship"> | |
170 <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"> | |
171 <option value="score">Based on score</option> | |
172 <option value="none" selected="true">Ignore score</option> | |
173 </param> | |
174 <when value="none"> | |
175 <!-- When no scaling is done, no scores available, then just let the | |
176 user choose a base color for the track --> | |
177 <expand macro="auto_color" /> | |
178 </when> | |
179 <when value="score"> | |
180 <!-- Scaling --> | |
181 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling" | |
182 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."> | |
183 <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option> | |
184 <option value="logarithmic" selected="" >Logarithmic scaling</option> | |
185 <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option> | |
186 </param> | |
187 | |
188 <!-- Scaling Bounds --> | |
189 <conditional name="score_scales" label="Minimum/Maximum values for track scores"> | |
190 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select"> | |
191 <option value="automatic" selected="true">Automatically determined</option> | |
192 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option> | |
193 </param> | |
194 <when value="automatic"> | |
195 </when> | |
196 <when value="manual"> | |
197 <param label="Minimum expected score" name="minimum" type="integer" value="0" /> | |
198 <param label="Maximum expected score" name="maximum" type="integer" value="100" /> | |
199 </when> | |
200 </conditional> | |
201 | |
202 <!-- Scale color --> | |
203 <conditional name="color_scheme" label="Color Scheme for scored features"> | |
204 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme"> | |
205 <option value="opacity">Opacity (high scores = 1.0 opacity)</option> | |
206 <!--<option value="brewer">Brewer Color Schemes</option>--> | |
207 </param> | |
208 <when value="opacity"> | |
209 <!-- Single color selection mode --> | |
210 <expand macro="auto_color" /> | |
211 </when> | |
212 <!--<when value="brewer">--> | |
213 <!--[> Brewer continuum selection <]--> | |
214 <!--<expand macro="brewer_scheme" />--> | |
215 <!--</when>--> | |
216 </conditional> | |
217 </when> | |
218 </conditional> | |
219 </section> | |
220 </xml> | |
221 <xml name="track_styling" | |
222 token_classname="feature" | |
223 token_label="name,id" | |
224 token_description="note,description" | |
225 token_height="100px"> | |
226 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> | |
227 <param label="JBrowse style.className" type="text" | |
228 name="style_classname" | |
229 value="@CLASSNAME@" | |
230 help="Set CSS style.className property"/> | |
231 <param label="JBrowse style.label" | |
232 type="text" | |
233 name="style_label" | |
234 value="@LABEL@" | |
235 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'" /> | |
236 <param label="JBrowse style.description" | |
237 type="text" | |
238 name="style_description" | |
239 value="@DESCRIPTION@" | |
240 help="Comma-separated list of case-insensitive feature tags to check for the feature's long description. The first one found will be used."/> | |
241 <param label="JBrowse style.height" | |
242 type="text" | |
243 name="style_height" | |
244 value="@HEIGHT@" | |
245 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."/> | |
246 </section> | |
247 </xml> | |
248 | |
249 <xml name="input_conditional" token_label="Track Data" token_format="data"> | |
250 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/> | |
251 </xml> | |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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changeset
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252 </macros> |