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comparison macros.xml @ 45:665c4f3e48ae draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
author iuc
date Wed, 15 Nov 2017 15:14:41 -0500
parents 976731ca823c
children 6b91a500c96d
comparison
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44:86728aa7f499 45:665c4f3e48ae
10 <requirement type="package" version="3.11">pyyaml</requirement> 10 <requirement type="package" version="3.11">pyyaml</requirement>
11 <yield/> 11 <yield/>
12 </requirements> 12 </requirements>
13 </xml> 13 </xml>
14 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> 14 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
15 <token name="@WRAPPER_VERSION@">0.5.3</token> 15 <token name="@WRAPPER_VERSION@">0.7.0</token>
16 <xml name="stdio"> 16 <xml name="stdio">
17 <stdio> 17 <stdio>
18 <exit_code range="1:"/> 18 <exit_code range="1:"/>
19 <exit_code range=":-1"/> 19 <exit_code range=":-1"/>
20 <regex match="Error:"/> 20 <regex match="Error:"/>
25 **Attribution** 25 **Attribution**
26 26
27 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche 27 This Galaxy tool relies on the JBrowse, maintained by the GMOD Community. The Galaxy wrapper is developed by Eric Rasche
28 ]]> 28 ]]>
29 </token> 29 </token>
30
31 <xml name="genome_selector"
32 token_help=""
33 token_label="Fasta sequences"
34 token_optional="False" >
35 <conditional name="reference_genome">
36 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
37 <option selected="True" value="indexed">Use a built-in genome</option>
38 <option value="history">Use a genome from history</option>
39 </param>
40 <when value="indexed">
41 <param
42 help="@HELP@"
43 label="@LABEL@"
44 name="genomes"
45 type="select"
46 optional="@OPTIONAL@"
47 >
48 <options from_data_table="all_fasta">
49 <filter column="2" type="sort_by" />
50 <validator message="No genomes are available for the selected input dataset" type="no_options" />
51 </options>
52 </param>
53 </when>
54 <when value="history">
55 <param
56 format="fasta"
57 label="@LABEL@"
58 help="@HELP@"
59 name="genomes"
60 type="data"
61 optional="@OPTIONAL@"
62 multiple="True" />
63 </when>
64 </conditional>
65 </xml>
66
30 <xml name="auto_manual_tk" 67 <xml name="auto_manual_tk"
31 token_cond_label="Color" 68 token_cond_label="Color"
32 token_cond_name="color" 69 token_cond_name="color"
33 token_select_label="Color Specification" 70 token_select_label="Color Specification"
34 token_select_name="color_select" 71 token_select_name="color_select"
51 <param type="select" label="Track Visibility" name="track_visibility"> 88 <param type="select" label="Track Visibility" name="track_visibility">
52 <option value="default_off">Off for new users</option> 89 <option value="default_off">Off for new users</option>
53 <option value="default_on">On for new users</option> 90 <option value="default_on">On for new users</option>
54 <option value="force">Force On</option> 91 <option value="force">Force On</option>
55 <option value="always">Always On (ignores URL parameters)</option> 92 <option value="always">Always On (ignores URL parameters)</option>
93 </param>
94 <param type="select" label="Override Apollo Plugins" name="override_apollo_plugins" help="Disable the apollo plugin for this track, this disables the ability to make an annotation from this feature.">
95 <option value="True">Yes - Override</option>
96 <option value="False" selected="True">No - Do not Override</option>
97 </param>
98 <param type="select" label="Override Apollo Draggability" name="override_apollo_drag" help="Disable apollo's drag-to-create feature functionality.">
99 <option value="True">Yes - Override</option>
100 <option value="False" selected="True">No - Do not Override</option>
56 </param> 101 </param>
57 </xml> 102 </xml>
58 103
59 <xml name="jb_color" 104 <xml name="jb_color"
60 token_label="JBrowse style.color" 105 token_label="JBrowse style.color"
177 </when> 222 </when>
178 <when value="score"> 223 <when value="score">
179 <!-- Scaling --> 224 <!-- Scaling -->
180 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling" 225 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
181 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."> 226 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.">
182 <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option> 227 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option>
183 <option value="logarithmic">Logarithmic scaling</option> 228 <option value="logarithmic" selected="false">Logarithmic scaling</option>
184 <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option> 229 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option>
185 </param> 230 </param>
186 231
187 <!-- Scaling Bounds --> 232 <!-- Scaling Bounds -->
188 <conditional name="score_scales" label="Minimum/Maximum values for track scores"> 233 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
189 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select"> 234 <param type="select" label="How should minimum and maximum values be determined for the scores of the features" name="scale_select">
217 </conditional> 262 </conditional>
218 </section> 263 </section>
219 </xml> 264 </xml>
220 <xml name="track_styling" 265 <xml name="track_styling"
221 token_classname="feature" 266 token_classname="feature"
222 token_label="name,id" 267 token_label="product,name,id"
223 token_description="note,description" 268 token_description="note,description"
224 token_height="100px"> 269 token_height="10px"
270 token_maxheight="600">
225 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> 271 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
226 <param label="JBrowse style.className" type="text" 272 <param label="JBrowse style.className" type="text"
227 name="style_classname" 273 name="style_classname"
228 value="@CLASSNAME@" 274 value="@CLASSNAME@"
229 help="Set CSS style.className property"/> 275 help="Set CSS style.className property"/>
240 <param label="JBrowse style.height" 286 <param label="JBrowse style.height"
241 type="text" 287 type="text"
242 name="style_height" 288 name="style_height"
243 value="@HEIGHT@" 289 value="@HEIGHT@"
244 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."/> 290 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."/>
291 <param label="JBrowse maxHeight"
292 type="text"
293 name="max_height"
294 value="@MAXHEIGHT@"
295 help="Maximum height that the track is permitted to reach in pixels."/>
245 </section> 296 </section>
246 </xml> 297 </xml>
247 298
248 <xml name="track_menu"> 299 <xml name="track_menu">
249 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false"> 300 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">