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comparison annotateviz.xml @ 0:7537482eed36 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotateviz commit 9bbaa3eacc76ff3bf2b6da313cc0d85705f15dd1-dirty
author eduardo
date Sat, 17 Jun 2017 13:31:06 -0400
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children ce990f818362
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-1:000000000000 0:7537482eed36
1 <tool id="annotateviz" name="AnnotateViz" version="0.1">
2 <description>Annotation tool for transcriptomes</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <command><![CDATA[
9 mkdir -p $output.files_path &&
10 ## Once that's done, we run the python script to handle the real work
11 python $__tool_directory__/jbrowse.py
12 --jbrowse \${JBROWSE_SOURCE_DIR}
13 --standalone
14 --outdir $output.files_path
15 $trackxml &&
16 mv $output.files_path/index.html $output;
17 python $__tool_directory__/annotateviz.py $db > $__tool_directory__/trans.json;
18
19 #sed "s@input_db@${__app__.security.encode_id($db.id)}@" $__tool_directory__/static/trinotateviz.html > $output;
20 mkdir ${output.files_path};
21 cp $__tool_directory__/static/js/gff_app.js ${output.files_path};
22 cp $__tool_directory__/static/css/main.css ${output.files_path};
23 cp $__tool_directory__/static/trans.json ${output.files_path}
24
25 ]]></command>
26 <configfiles>
27 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
28 <root>
29 <metadata>
30 <gencode>1</gencode>
31 <genomes>
32 <genome>$genome</genome>
33 </genomes>
34 <general>
35 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
36 <trackPadding>${jbgen.trackPadding}</trackPadding>
37
38 <shareLink>${jbgen.shareLink}</shareLink>
39 <aboutDescription>${jbgen.aboutDescription}</aboutDescription>
40 <show_tracklist>${jbgen.show_tracklist}</show_tracklist>
41 <show_nav>${jbgen.show_nav}</show_nav>
42 <show_overview>${jbgen.show_overview}</show_overview>
43 <show_menu>${jbgen.show_menu}</show_menu>
44 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions>
45 </general>
46 </metadata>
47 <tracks>
48 #for $tg in $track_groups:
49 #for $track in $tg.data_tracks:
50 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}">
51 <files>
52 #for $dataset in $track.data_format.annotation:
53 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}" />
54 #end for
55 </files>
56 <options>
57 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast":
58 <style>
59 <className>${track.data_format.jbstyle.style_classname}</className>
60 <description>${track.data_format.jbstyle.style_description}</description>
61 <label>${track.data_format.jbstyle.style_label}</label>
62 <height>${track.data_format.jbstyle.style_height}</height>
63 </style>
64 <scaling>
65 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none":
66 <method>ignore</method>
67 <scheme>
68 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic":
69 <color>__auto__</color>
70 #else
71 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color>
72 #end if
73 </scheme>
74 #else
75 <method>score</method>
76 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo>
77 <scales>
78 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type>
79 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual":
80 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min>
81 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max>
82 #end if
83 </scales>
84 <scheme>
85 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type>
86 ## auto_color
87 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity":
88 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic":
89 <color>__auto__</color>
90 #else
91 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color>
92 #end if
93 #end if
94 </scheme>
95 #end if
96 </scaling>
97 <menus>
98 #for $menu_item in $track.data_format.jbmenu.track_menu:
99 <menu>
100 <action>${menu_item.menu_action}</action>
101 #if str($menu_item.menu_label) != "":
102 <label>${menu_item.menu_label}</label>
103 #end if
104 #if str($menu_item.menu_title) != "":
105 <title>${menu_item.menu_title}</title>
106 #end if
107 #if str($menu_item.menu_url) != "":
108 <url>${menu_item.menu_url.replace("&", "&amp;").replace("\"", "&quot;")}</url>
109 #end if
110 #if str($menu_item.menu_icon) != "":
111 <iconClass>${menu_item.menu_icon}</iconClass>
112 #end if
113 </menu>
114 #end for
115 </menus>
116 #end if
117 #if str($track.data_format.data_format_select) == "wiggle":
118 <wiggle>
119 <type>${track.data_format.xyplot}</type>
120 <variance_band>${track.data_format.var_band}</variance_band>
121 #if str($track.data_format.scaling.scale_select) == "auto_local":
122 <autoscale>local</autoscale>
123 #else if str($track.data_format.scaling.scale_select) == "auto_global":
124 <autoscale>global</autoscale>
125 #else:
126 <min>${track.data_format.scaling.minimum}</min>
127 <max>${track.data_format.scaling.maximum}</max>
128 #end if
129 ## Wiggle tracks need special color config
130 #if str($track.data_format.jbcolor.color.color_select) != "automatic":
131 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos>
132 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg>
133 #else:
134 <color_pos>__auto__</color_pos>
135 <color_neg>__auto__</color_neg>
136 #end if
137 ## Bicolor pivot config
138 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero":
139 <bicolor_pivot>zero</bicolor_pivot>
140 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean":
141 <bicolor_pivot>mean</bicolor_pivot>
142 #else:
143 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot>
144 #end if
145 </wiggle>
146 #else if str($track.data_format.data_format_select) == "pileup":
147 <pileup>
148 <auto_snp>${track.data_format.auto_snp}</auto_snp>
149 <bam_indices>
150 #for $dataset in $track.data_format.annotation:
151 <bam_index>${dataset.metadata.bam_index}</bam_index>
152 #end for
153 </bam_indices>
154 </pileup>
155 #else if str($track.data_format.data_format_select) == "blast":
156 <blast>
157 #if str($track.data_format.blast_parent) != "":
158 <parent>${track.data_format.blast_parent}</parent>
159 #end if
160 <protein>${track.data_format.is_protein}</protein>
161 <min_gap>${track.data_format.min_gap}</min_gap>
162 <index>${track.data_format.index}</index>
163 </blast>
164 #else if str($track.data_format.data_format_select) == "gene_calls":
165 <gff>
166 <trackType>${track.data_format.track_config.track_class}</trackType>
167 #if $track.data_format.track_config.track_class == 'JBrowse/View/Track/CanvasFeatures':
168 #if str($track.data_format.track_config.canvas_options.transcriptType) != "":
169 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType>
170 #end if
171 #if str($track.data_format.track_config.canvas_options.subParts) != "":
172 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts>
173 #end if
174 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false":
175 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs>
176 #end if
177 #else if $track.data_format.track_config.track_class == 'JBrowse/View/Track/HTMLFeatures':
178 #if str($track.data_format.track_config.html_options.transcriptType) != "":
179 <transcriptType>${track.data_format.track_config.html_options.transcriptType}</transcriptType>
180 #end if
181 #end if
182 #if $track.data_format.match_part.match_part_select:
183 <match>${track.data_format.match_part.name}</match>
184 #end if
185 <index>${track.data_format.index}</index>
186 </gff>
187 ## #else if str($track.data_format.data_format_select) == "sparql":
188 ## <sparql>
189 ## <url>${track.data_format.url}</url>
190 ## <label>${track.data_format.label}</label>
191 ## <!-- This is going to be an absolutey nightmare -->
192 ## <query>${track.data_format.query}</query>
193 ## </sparql>
194 #end if
195 </options>
196 </track>
197 #end for
198 #end for
199 </tracks>
200 </root>
201 ]]></configfile>
202 </configfiles>
203 <inputs>
204 <param name="db" type="data" format="sqlite" />
205 <param name="genome" type="data" format="fasta" optional="false" label="Peptide predictions" help="Predicted peptides in fasta format" />
206 <repeat name="track_groups" title="Track Group">
207 <param label="Track Category"
208 name="category"
209 type="text"
210 value="Default"
211 help="Organise your tracks into Categories for a nicer end-user experience" optional="False"/>
212 <repeat name="data_tracks" title="Annotation Track">
213 <conditional name="data_format">
214 <param type="select" label="Track Type" name="data_format_select">
215 <option value="gene_calls">GFF/GFF3/BED/GBK Features</option>
216 <option value="pileup">BAM Pileups</option>
217 <option value="blast">Blast XML</option>
218 <option value="wiggle">BigWig XY</option>
219 <option value="vcf">VCF SNPs</option>
220 <!--<option value="sparql">SPARQL</option>-->
221 </param>
222 <when value="blast">
223 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" />
224
225 <param label="Features used in Blast Search"
226 help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."
227 format="gff3"
228 name="blast_parent"
229 optional="true"
230 type="data"/>
231
232 <param label="Minimum Gap Size"
233 help="before a new match_part feature is created"
234 name="min_gap"
235 type="integer"
236 value="10"
237 min="2" />
238 <param label="Is this a protein blast search?"
239 type="boolean"
240 name="is_protein"
241 truevalue="true"
242 falsevalue="false" />
243
244 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
245
246 <expand macro="track_styling"
247 classname="feature"
248 label="description"
249 description="Hit_titles"
250 height="600px"/>
251 <expand macro="color_selection"
252 token_scaling_lin_select="false"
253 token_scaling_log_select="true" />
254 <expand macro="track_menu" />
255 <expand macro="track_display" />
256 </when>
257 <when value="vcf">
258 <expand macro="input_conditional" label="SNP Track Data" format="vcf" />
259 <expand macro="track_display" />
260 </when>
261 <when value="gene_calls">
262 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" />
263 <conditional name="match_part">
264 <param label="This is match/match_part data"
265 type="boolean"
266 name="match_part_select"
267 truevalue="true"
268 falsevalue="false" />
269 <when value="true">
270 <param label="Match Part Feature Type"
271 name="name"
272 type="text"
273 value="match"
274 help="Match_parts have several options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here"
275 optional="False"/>
276 </when>
277 <when value="false" />
278 </conditional>
279
280 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" />
281
282 <conditional name="track_config">
283 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class">
284 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option>
285 <option value="JBrowse/View/Track/CanvasFeatures" selected="true">Canvas Features</option>
286 </param>
287 <when value="JBrowse/View/Track/CanvasFeatures">
288 <section name="canvas_options" title="CanvasFeatures Options [Advanced]" expanded="false">
289 <param label="Transcript type"
290 name="transcriptType"
291 type="text"
292 value=""
293 help="If your input files represents transcripts with features not named 'mRNA', give the alternate name here (e.g. 'transcript')"
294 optional="True"/>
295 <param label="Subfeatures type"
296 name="subParts"
297 type="text"
298 value=""
299 help="If you have 'exons' but no corresponding 'CDS' features, specify here the subfeatures that should be displayed (e.g. 'exon')"
300 optional="True"/>
301 <param label="Implied UTRs"
302 name="impliedUTRs"
303 type="boolean"
304 checked="false"
305 truevalue="true"
306 falsevalue="false"
307 help="Check this your input files does not contain UTR features, but the UTR can be 'implied' from the difference between the exon and CDS boundaries"/>
308 </section>
309 </when>
310 <when value="JBrowse/View/Track/HTMLFeatures">
311 <section name="html_options" title="HTMLFeatures Options [Advanced]" expanded="false">
312 <param label="Transcript type"
313 name="transcriptType"
314 type="text"
315 value=""
316 help="If your input files represents transcripts, give the name of the corresponding features here (e.g. 'mRNA' or 'transcript')"
317 optional="True"/>
318 </section>
319 </when>
320 </conditional>
321 <expand macro="track_styling" />
322 <expand macro="color_selection" />
323 <expand macro="track_menu" />
324 <expand macro="track_display" />
325 </when>
326 <when value="pileup">
327 <expand macro="input_conditional" label="BAM Track Data" format="bam" />
328 <param label="Autogenerate SNP Track"
329 help="Not recommended for deep coverage BAM files"
330 type="boolean"
331 name="auto_snp"
332 truevalue="true"
333 falsevalue="false" />
334 <expand macro="track_display" />
335 </when>
336 <when value="wiggle">
337 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" />
338
339 <param label="Use XYPlot"
340 help="instead of continuous colored band"
341 type="boolean"
342 name="xyplot"
343 truevalue="JBrowse/View/Track/Wiggle/XYPlot"
344 falsevalue="JBrowse/View/Track/Wiggle/Density" />
345 <param label="Show variance band"
346 help="Only for XYPlots"
347 type="boolean"
348 name="var_band"
349 truevalue="true"
350 falsevalue="false" />
351
352 <conditional name="scaling">
353 <param type="select" label="Track Scaling" name="scale_select">
354 <option value="auto_local">Autoscale (local)</option>
355 <option value="auto_global" selected="true">Autoscale (global)</option>
356 <option value="fixed">Specify Min/Max</option>
357 </param>
358 <when value="auto_local"></when>
359 <when value="auto_global"></when>
360 <when value="fixed">
361 <param label="Track minimum" name="minimum"
362 type="integer" value="0" />
363 <param label="Track maximum" name="maximum"
364 type="integer" value="100" />
365 </when>
366 </conditional>
367 <expand macro="color_selection_minmax" />
368 <expand macro="track_display" />
369 </when>
370 <!--
371 <when value="sparql">
372 <param type="text" label="SPARQL Server URL" name="url" />
373 <param type="text" label="Track Label" name="key" value="SPARQL Genes" />
374 <param type="text" label="SPARQL Query" name="query" area="true" />
375 <expand macro="track_display" />
376 </when>
377 -->
378 </conditional>
379 </repeat>
380 </repeat>
381
382 <expand macro="general_options" />
383 <param type="hidden" name="uglyTestingHack" value="" />
384 </inputs>
385 <outputs>
386 <data format="html" name="output" label="Annotateviz $on_string "/>
387
388 </outputs>
389 <tests>
390 <test>
391 <param name="db" value="Trinotate_no_uniprot.sqlite" />
392 <output name="output" file="trinotateviz.html" lines_diff="2" />
393 </test>
394 </tests>
395 <help><![CDATA[
396
397
398
399 @ATTRIBUTION@
400 ]]></help>
401 <expand macro="citations"/>
402 </tool>