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comparison macros.xml @ 8:ad4b9d7eae6a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
author iuc
date Tue, 29 Nov 2016 10:55:30 -0500
parents ecbdfc775b9a
children 1a6d882d340d
comparison
equal deleted inserted replaced
7:1e74f16adaa1 8:ad4b9d7eae6a
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="1.12.0">jbrowse</requirement> 5 <requirement type="package" version="1.12.1">jbrowse</requirement>
6 <requirement type="package" version="1.12.0">bundle_jbrowse</requirement>
7 <requirement type="package" version="2.7">python</requirement> 6 <requirement type="package" version="2.7">python</requirement>
8 <requirement type="package" version="5.18.1">perl</requirement>
9 <requirement type="package" version="1.66">biopython</requirement> 7 <requirement type="package" version="1.66">biopython</requirement>
10 <requirement type="package" version="0.6.2">bcbiogff</requirement> 8 <requirement type="package" version="0.6.2">bcbiogff</requirement>
11 <requirement type="package" version="1.2">samtools</requirement> 9 <requirement type="package" version="1.2">samtools</requirement>
12 <requirement type="package" version="3.11">pyyaml</requirement> 10 <requirement type="package" version="3.11">pyyaml</requirement>
13 <yield/> 11 <yield/>
14 </requirements> 12 </requirements>
15 </xml> 13 </xml>
16 <token name="@WRAPPER_VERSION@">1.0</token> 14 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
15 <token name="@WRAPPER_VERSION@">0.5.1</token>
17 <xml name="stdio"> 16 <xml name="stdio">
18 <stdio> 17 <stdio>
19 <exit_code range="1:"/> 18 <exit_code range="1:"/>
20 <exit_code range=":-1"/> 19 <exit_code range=":-1"/>
21 <regex match="Error:"/> 20 <regex match="Error:"/>
26 **Attribution** 25 **Attribution**
27 26
28 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
29 ]]> 28 ]]>
30 </token> 29 </token>
31
32 <xml name="genome_selector"
33 token_help=""
34 token_label="Fasta sequences"
35 token_optional="False" >
36 <conditional name="reference_genome">
37 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select">
38 <option selected="True" value="indexed">Use a built-in genome</option>
39 <option value="history">Use a genome from history</option>
40 </param>
41 <when value="indexed">
42 <param
43 help="@HELP@"
44 label="@LABEL@"
45 name="genomes"
46 type="select"
47 optional="@OPTIONAL@"
48 >
49 <options from_data_table="all_fasta">
50 <filter column="2" type="sort_by" />
51 <validator message="No genomes are available for the selected input dataset" type="no_options" />
52 </options>
53 </param>
54 </when>
55 <when value="history">
56 <param
57 format="fasta"
58 label="@LABEL@"
59 help="@HELP@"
60 name="genomes"
61 type="data"
62 optional="@OPTIONAL@"
63 multiple="True" />
64 </when>
65 </conditional>
66 </xml>
67
68 <xml name="auto_manual_tk" 30 <xml name="auto_manual_tk"
69 token_cond_label="Color" 31 token_cond_label="Color"
70 token_cond_name="color" 32 token_cond_name="color"
71 token_select_label="Color Specification" 33 token_select_label="Color Specification"
72 token_select_name="color_select" 34 token_select_name="color_select"
216 <when value="score"> 178 <when value="score">
217 <!-- Scaling --> 179 <!-- Scaling -->
218 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling" 180 <param type="select" label="JBrowse style.color function's score scaling" name="score_scaling"
219 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."> 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.">
220 <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option> 182 <option value="linear" selected="@SCALING_LIN_SELECT@" >Linear scaling</option>
221 <option value="logarithmic" selected="" >Logarithmic scaling</option> 183 <option value="logarithmic">Logarithmic scaling</option>
222 <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option> 184 <option value="blast" selected="@SCALING_LOG_SELECT@" >Blast scaling</option>
223 </param> 185 </param>
224 186
225 <!-- Scaling Bounds --> 187 <!-- Scaling Bounds -->
226 <conditional name="score_scales" label="Minimum/Maximum values for track scores"> 188 <conditional name="score_scales" label="Minimum/Maximum values for track scores">
255 </conditional> 217 </conditional>
256 </section> 218 </section>
257 </xml> 219 </xml>
258 <xml name="track_styling" 220 <xml name="track_styling"
259 token_classname="feature" 221 token_classname="feature"
260 token_label="prodcut,name,id" 222 token_label="name,id"
261 token_description="note" 223 token_description="note,description"
262 token_height="100px"> 224 token_height="100px">
263 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> 225 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false">
264 <param label="JBrowse style.className" type="text" 226 <param label="JBrowse style.className" type="text"
265 name="style_classname" 227 name="style_classname"
266 value="@CLASSNAME@" 228 value="@CLASSNAME@"
281 value="@HEIGHT@" 243 value="@HEIGHT@"
282 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."/> 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."/>
283 </section> 245 </section>
284 </xml> 246 </xml>
285 247
248 <xml name="track_menu">
249 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false">
250 <repeat name="track_menu" title="Track Menu">
251 <param label="Menu action"
252 type="select"
253 name="menu_action"
254 help="Action performed when user clicks on the menu">
255 <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option>
256 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option>
257 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option>
258 </param>
259 <param label="Menu label"
260 type="text"
261 name="menu_label"
262 help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
263 <expand macro="menu_sanitize" />
264 </param>
265 <param label="Menu title"
266 type="text"
267 name="menu_title"
268 help="Will be displayed in the popup title bar if displayed ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
269 <expand macro="menu_sanitize" />
270 </param>
271 <param label="Menu url"
272 type="text"
273 name="menu_url"
274 help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)">
275 <expand macro="menu_sanitize" />
276 </param>
277 <param label="Menu icon"
278 type="select"
279 name="menu_icon"
280 help="Icon to display next to menu label">
281 <option value="dijitIconBookmark" selected="true">Bookmark</option>
282 <option value="dijitIconSave">Save</option>
283 <option value="dijitIconPrint">Print</option>
284 <option value="dijitIconCut">Cut</option>
285 <option value="dijitIconCopy">Copy</option>
286 <option value="dijitIconClear">Clear</option>
287 <option value="dijitIconDelete">Delete</option>
288 <option value="dijitIconUndo">Undo</option>
289 <option value="dijitIconEdit">Edit</option>
290 <option value="dijitIconNewTask">New Task</option>
291 <option value="dijitIconEditTask">Edit Task</option>
292 <option value="dijitIconEditProperty">Edit Property</option>
293 <option value="dijitIconTask">Task</option>
294 <option value="dijitIconFilter">Filter</option>
295 <option value="dijitIconConfigure">Configure</option>
296 <option value="dijitIconSearch">Search</option>
297 <option value="dijitIconApplication">Application</option>
298 <option value="dijitIconChart">Chart</option>
299 <option value="dijitIconConnector">Connector</option>
300 <option value="dijitIconDatabase">Database</option>
301 <option value="dijitIconDocuments">Documents</option>
302 <option value="dijitIconMail">Mail</option>
303 <option value="dijitLeaf">Leaf</option>
304 <option value="dijitIconFile">File</option>
305 <option value="dijitIconFunction">Function</option>
306 <option value="dijitIconKey">Key</option>
307 <option value="dijitIconPackage">Package</option>
308 <option value="dijitIconSample">Sample</option>
309 <option value="dijitIconTable">Table</option>
310 <option value="dijitIconUsers">Users</option>
311 <option value="dijitIconFolderClosed">Folder Closed</option>
312 <option value="dijitIconFolderOpen">Folder Open</option>
313 <option value="dijitIconError">Error</option>
314 </param>
315 </repeat>
316 </section>
317 </xml>
318
319 <xml name="menu_sanitize">
320 <sanitizer>
321 <valid>
322 <add value="{"/>
323 <add value="}"/>
324 <add value="!"/>
325 <add value="?"/>
326 <add value="&amp;"/>
327 <add value="+"/>
328 <add value="="/>
329 <add value="'"/>
330 <add value='"'/>
331 </valid>
332 </sanitizer>
333 </xml>
334
286 <xml name="input_conditional" token_label="Track Data" token_format="data"> 335 <xml name="input_conditional" token_label="Track Data" token_format="data">
287 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/> 336 <param label="@LABEL@" format="@FORMAT@" name="annotation" type="data" multiple="True"/>
288 </xml> 337 </xml>
338 <xml name="citations">
339 <citations>
340 <citation type="doi">10.1101/gr.094607.109</citation>
341 </citations>
342 </xml>
289 </macros> 343 </macros>