Mercurial > repos > iuc > jbrowse
annotate macros.xml @ 30:12d5699f92e9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
| author | iuc |
|---|---|
| date | Sat, 25 Jun 2016 15:07:08 -0400 |
| parents | 5614cf75bb24 |
| children | ce9d92980c78 |
| rev | line source |
|---|---|
|
0
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
2 <macros> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
3 <xml name="requirements"> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
4 <requirements> |
| 16 | 5 <requirement type="package" version="1.12.0">jbrowse</requirement> |
| 26 | 6 <requirement type="package" version="1.12.0">bundle_jbrowse</requirement> |
|
13
67fb31daef0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents:
12
diff
changeset
|
7 <requirement type="package" version="2.7">python</requirement> |
| 24 | 8 <requirement type="package" version="5.18.1">perl</requirement> |
| 16 | 9 <requirement type="package" version="1.66">biopython</requirement> |
| 10 <requirement type="package" version="0.6.2">bcbiogff</requirement> | |
|
13
67fb31daef0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents:
12
diff
changeset
|
11 <requirement type="package" version="1.2">samtools</requirement> |
|
67fb31daef0e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 399061eca3a2956704522974446601755503c96d-dirty
iuc
parents:
12
diff
changeset
|
12 <requirement type="package" version="3.11">pyyaml</requirement> |
|
0
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
13 <yield/> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
14 </requirements> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
15 </xml> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
16 <token name="@WRAPPER_VERSION@">1.0</token> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
17 <xml name="stdio"> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
18 <stdio> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
19 <exit_code range="1:"/> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
20 <exit_code range=":-1"/> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
21 <regex match="Error:"/> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
22 <regex match="Exception:"/> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
23 </stdio> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
24 </xml> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
25 <token name="@ATTRIBUTION@"><![CDATA[ |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
26 **Attribution** |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
27 |
| 29 | 28 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche |
|
0
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
29 ]]> |
|
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
30 </token> |
| 16 | 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 | |
|
30
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
51 <xml name="track_display"> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
52 <param type="select" label="Track Visibility" name="track_visibility"> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
53 <option value="default_off">Off for new users</option> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
54 <option value="default_on">On for new users</option> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
55 <option value="force">Force On</option> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
56 <option value="always">Always On (ignores URL parameters)</option> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
57 </param> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
58 </xml> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
59 |
| 16 | 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" | |
| 29 | 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"> | |
| 16 | 82 <expand macro="auto_manual_tk" |
| 29 | 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@"> | |
| 16 | 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> | |
|
30
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
109 <xml name="general_options"> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
110 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
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'"/> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
112 <param label="Track Padding" type="integer" value="20" name="trackPadding" help="Spacing between tracks in the genome view, in pixels." /> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
113 |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
114 <param label="Enable Share Link" name="shareLink" type="boolean" checked="true" truevalue="true" falsevalue="false" /> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
115 <param label="About the Browser" type="text" name="aboutDescription" value="" help="Description of the browser to be used in the 'About' popup" /> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
116 |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
117 <param label="Show Track List" name="show_tracklist" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the track list"/> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
118 <param label="Show Navigation" name="show_nav" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the navigation menu"/> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
119 <param label="Show Overview" name="show_overview" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the overview bar"/> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
120 <param label="Show Menu" name="show_menu" type="boolean" checked="true" truevalue="true" falsevalue="false" help="Optionally hide the menu bar"/> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
121 |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
122 <param label="Hide Genome Options" name="hideGenomeOptions" type="boolean" truevalue="true" falsevalue="false" help="Hide options for opening a sequence file"/> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
123 </section> |
|
12d5699f92e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
29
diff
changeset
|
124 </xml> |
| 16 | 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" | |
| 29 | 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." /> | |
| 16 | 142 <expand macro="jb_color" |
| 29 | 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." /> | |
| 16 | 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" | |
| 29 | 165 token_scaling_lin_select="true" |
| 166 token_scaling_log_select="false" | |
| 16 | 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" | |
| 29 | 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."> |
| 16 | 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" | |
| 29 | 222 token_classname="feature" |
| 223 token_label="name,id" | |
| 224 token_description="note,description" | |
| 225 token_height="100px"> | |
| 16 | 226 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
| 227 <param label="JBrowse style.className" type="text" | |
| 29 | 228 name="style_classname" |
| 229 value="@CLASSNAME@" | |
| 230 help="Set CSS style.className property"/> | |
| 16 | 231 <param label="JBrowse style.label" |
| 29 | 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'" /> | |
| 16 | 236 <param label="JBrowse style.description" |
| 29 | 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."/> | |
| 16 | 241 <param label="JBrowse style.height" |
| 29 | 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."/> | |
| 16 | 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> | |
|
0
c77c1d5baadb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 25797deb85d5b7582b8ee11076998622bc282fd8
iuc
parents:
diff
changeset
|
252 </macros> |