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comparison macros.xml @ 3:7342f467507b draft

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Uploaded v0.4 of JBrowse
author iuc
date Thu, 31 Dec 2015 13:58:43 -0500
parents b6a0e126dbee
children ae9382cfb6ac
comparison
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2:b6a0e126dbee 3:7342f467507b
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.11.6">jbrowse</requirement> 5 <requirement type="package" version="1.12.0">jbrowse</requirement>
6 <requirement type="package" version="1.12.0">bundle_jbrowse</requirement>
6 <requirement type="package" version="2.7">python</requirement> 7 <requirement type="package" version="2.7">python</requirement>
7 <requirement type="package" version="5.18">perl</requirement> 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>
8 <requirement type="package" version="1.2">samtools</requirement> 11 <requirement type="package" version="1.2">samtools</requirement>
9 <requirement type="package" version="1.0">bundle_jbrowse</requirement>
10 <requirement type="package" version="3.11">pyyaml</requirement> 12 <requirement type="package" version="3.11">pyyaml</requirement>
11 <yield/> 13 <yield/>
12 </requirements> 14 </requirements>
13 </xml> 15 </xml>
14 <token name="@WRAPPER_VERSION@">1.0</token> 16 <token name="@WRAPPER_VERSION@">1.0</token>
21 </stdio> 23 </stdio>
22 </xml> 24 </xml>
23 <token name="@ATTRIBUTION@"><![CDATA[ 25 <token name="@ATTRIBUTION@"><![CDATA[
24 **Attribution** 26 **Attribution**
25 27
26 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community 28 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
27 ]]> 29 ]]>
28 </token> 30 </token>
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
51 <xml name="jb_color"
52 token_label="JBrowse style.color"
53 token_name="style_color"
54 token_value="goldenrod"
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"
56 >
57 <param label="@LABEL@" type="color" name="@NAME@" value="@VALUE@" help="@HELP@">
58 <sanitizer>
59 <valid initial="string.letters,string.digits">
60 <add value="#" />
61 </valid>
62 </sanitizer>
63 </param>
64 </xml>
65
66 <xml name="auto_color"
67 token_cond_label="Color"
68 token_cond_name="color"
69 token_select_label="Color Selection"
70 token_select_name="color_select"
71 token_automatic_label="Automatically selected"
72 token_manual_label="Manual Color Selection">
73 <expand macro="auto_manual_tk"
74 cond_label="@COND_LABEL@"
75 cond_name="@COND_NAME@"
76 select_label="@SELECT_LABEL@"
77 select_name="@SELECT_NAME@"
78 automatic_label="@AUTOMATIC_LABEL@"
79 manual_label="@MANUAL_LABEL@">
80 <expand macro="jb_color" />
81 <yield />
82 </expand>
83 </xml>
84
85
86
87 <xml name="brewer_scheme">
88 <param type="select" label="Brewer color Scheme" name="brewer_scheme">
89 <option value="BrBg">BrBg: Brown - Blue Green</option>
90 <option value="PiYg">PiYg: Pink - Yellow Green</option>
91 <option value="PRGn">PRGn: Purple Red - Green</option>
92 <option value="PuOr">PuOr: Purple - Orange</option>
93 <option value="RdBu" selected="true">RdBu: Red - Blue</option>
94 <option value="RdGy">RdGy: Red - Gray</option>
95 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option>
96 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option>
97 <option value="Spectral">Spectral</option>
98 </param>
99 </xml>
100 <xml name="color_selection_minmax">
101 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false">
102 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the
103 auto case as well, but may be safe to just say "brewer colors? Pff,
104 red/blue" -->
105 <expand macro="auto_manual_tk"
106 token_cond_label="Color"
107 token_cond_name="color"
108 token_select_label="Color Selection"
109 token_select_name="color_select"
110 token_automatic_label="Automatically selected"
111 token_manual_label="Manual Color Selection">
112 <expand macro="jb_color"
113 label="JBrowse style.pos_color"
114 name="style_pos_color"
115 value="blue"
116 help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point." />
117 <expand macro="jb_color"
118 label="JBrowse style.neg_color"
119 name="style_neg_color"
120 value="red"
121 help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point." />
122 </expand>
123
124 <conditional name="bicolor_pivot" label="Bicolor Pivot">
125 <param type="select" label="Bicolor Pivot" name="bicolor_pivot_select">
126 <option value="zero" selected="true">Zero</option>
127 <option value="mean">Mean</option>
128 <option value="custom">Custom Value</option>
129 </param>
130 <when value="zero" />
131 <when value="mean" />
132 <when value="custom">
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." />
134 </when>
135 </conditional>
136 </section>
137 </xml>
138
139 <xml name="color_selection"
140 token_scaling_lin_select="true"
141 token_scaling_log_select="false"
142 >
143 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling &amp; Coloring Options [Advanced]" expanded="false">
144 <conditional name="color_score" label="JBrowse style.color &amp; Score relationship">
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">
146 <option value="score">Based on score</option>
147 <option value="none" selected="true">Ignore score</option>
148 </param>
149 <when value="none">
150 <!-- When no scaling is done, no scores available, then just let the
151 user choose a base color for the track -->
152 <expand macro="auto_color" />
153 </when>
154 <when value="score">
155 <!-- Scaling -->
156 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
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.">
158 <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
159 <option value="logarithmic" selected="" >Logarithmic scaling</option>
160 <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
161 </param>
162
163 <!-- Scaling Bounds -->
164 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
165 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select">
166 <option value="automatic" selected="true">Automatically determined</option>
167 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option>
168 </param>
169 <when value="automatic">
170 </when>
171 <when value="manual">
172 <param label="Minimum expected score" name="minimum" type="integer" value="0" />
173 <param label="Maximum expected score" name="maximum" type="integer" value="100" />
174 </when>
175 </conditional>
176
177 <!-- Scale color -->
178 <conditional name="color_scheme" label="Color Scheme for scored features">
179 <param type="select" label="JBrowse style.color function's color scheme for scored values" name="score_scheme">
180 <option value="opacity">Opacity (high scores = 1.0 opacity)</option>
181 <!--<option value="brewer">Brewer Color Schemes</option>-->
182 </param>
183 <when value="opacity">
184 <!-- Single color selection mode -->
185 <expand macro="auto_color" />
186 </when>
187 <!--<when value="brewer">-->
188 <!--[> Brewer continuum selection <]-->
189 <!--<expand macro="brewer_scheme" />-->
190 <!--</when>-->
191 </conditional>
192 </when>
193 </conditional>
194 </section>
195 </xml>
196 <xml name="track_styling"
197 token_classname="feature"
198 token_label="name,id"
199 token_description="note,description"
200 token_height="100px">
201 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
202 <param label="JBrowse style.className" type="text"
203 name="style_classname"
204 value="@CLASSNAME@"
205 help="Set CSS style.className property"/>
206 <param label="JBrowse style.label"
207 type="text"
208 name="style_label"
209 value="@LABEL@"
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'" />
211 <param label="JBrowse style.description"
212 type="text"
213 name="style_description"
214 value="@DESCRIPTION@"
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."/>
216 <param label="JBrowse style.height"
217 type="text"
218 name="style_height"
219 value="@HEIGHT@"
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."/>
221 </section>
222 </xml>
223
224 <xml name="input_conditional" token_label="Track Data" token_format="data">
225 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
226 </xml>
29 </macros> 227 </macros>