Mercurial > repos > yating-l > jbrowsearchivecreator

comparison jbrowseArchiveCreator.xml @ 13:43a700afd457 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit bcb239c4045d2c47a8acad5fbd29eea03663e187
author yating-l
date Tue, 19 Jun 2018 17:59:51 -0400
parents 9161beae834f
children 3f9971a91096
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12:9161beae834f 13:43a700afd457
1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.1.5"> 1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.2.1">
2 <description> 2 <description>
3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin 3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
79 79
80 ## For each format, we have a few mandatory fields we store in a dict 80 ## For each format, we have a few mandatory fields we store in a dict
81 #set track_color = str($f.formatChoice.track_color) 81 #set track_color = str($f.formatChoice.track_color)
82 #set group_name = str($g.group_name) 82 #set group_name = str($g.group_name)
83 #set longLabel = str($f.formatChoice.longLabel) 83 #set longLabel = str($f.formatChoice.longLabel)
84
84 #set extra_data_dict = {"track_color": $track_color, 85 #set extra_data_dict = {"track_color": $track_color,
85 "group_name": $group_name, 86 "group_name": $group_name,
86 "long_label": $longLabel} 87 "long_label": $longLabel}
87 #if $f.formatChoice.format_select == "bam" 88 #if $f.formatChoice.format_select == "bam"
88 #set bam_index = $f.formatChoice.BAM.metadata.bam_index 89 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
89 90
90 ## Add Bam format specific fields 91 ## Add Bam format specific fields
91 #silent $extra_data_dict.update({"index": $bam_index}) 92 #silent $extra_data_dict.update({"index": $bam_index, "nameIndex": str($f.formatChoice.nameIndex)})
92 93
93 #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict) 94 #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
94 #end if 95 #end if
95 #if $f.formatChoice.format_select == "bed" 96 #if $f.formatChoice.format_select == "bed"
97 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.bedChoice.nameIndex)})
96 #if $f.formatChoice.bedChoice.bed_select == "bed_generic" 98 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
97 #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED_generic, $index_track_final, 99 #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED_generic, $index_track_final,
98 $extra_data_dict) 100 $extra_data_dict)
99 #end if 101 #end if
100 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" 102 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
117 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, 119 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
118 $extra_data_dict) 120 $extra_data_dict)
119 #end if 121 #end if
120 #end if 122 #end if
121 #if $f.formatChoice.format_select == "blastxml" 123 #if $f.formatChoice.format_select == "blastxml"
122 #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final, 124 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
125 #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final,
123 extra_data_dict) 126 extra_data_dict)
124 #end if 127 #end if
125 #if $f.formatChoice.format_select == "bigwig" 128 #if $f.formatChoice.format_select == "bigwig"
129 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
126 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final, 130 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
127 $extra_data_dict) 131 $extra_data_dict)
128 #end if 132 #end if
129 #if $f.formatChoice.format_select == 'gff3' 133 #if $f.formatChoice.format_select == 'gff3'
134 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
130 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final, 135 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
131 $extra_data_dict) 136 $extra_data_dict)
132 #end if 137 #end if
133 #if $f.formatChoice.format_select == "gtf" 138 #if $f.formatChoice.format_select == "gtf"
139 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
134 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 140 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
135 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final, 141 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
136 $extra_data_dict) 142 $extra_data_dict)
137 #end if 143 #end if
138 #end for 144 #end for
198 <valid initial="string.letters,string.digits"> 204 <valid initial="string.letters,string.digits">
199 <add value="#"/> 205 <add value="#"/>
200 </valid> 206 </valid>
201 </sanitizer> 207 </sanitizer>
202 </param> 208 </param>
209 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
203 </when> 210 </when>
204 <when value="bed"> 211 <when value="bed">
205 <conditional name="bedChoice"> 212 <conditional name="bedChoice">
206 <param name="bed_select" type="select" label="Bed Choice"> 213 <param name="bed_select" type="select" label="Bed Choice">
207 <option value="bed_generic">BED format</option> 214 <option value="bed_generic">BED Generic</option>
208 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> 215 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
209 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> 216 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
210 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option> 217 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
211 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option> 218 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
212 </param> 219 </param>
215 format="bed" 222 format="bed"
216 name="BED_generic" 223 name="BED_generic"
217 type="data" 224 type="data"
218 label="Bed File" 225 label="Bed File"
219 /> 226 />
227 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
220 </when> 228 </when>
221 <when value="bed_simple_repeats_option"> 229 <when value="bed_simple_repeats_option">
222 <param 230 <param
223 format="bed" 231 format="bed"
224 name="BED_simple_repeats" 232 name="BED_simple_repeats"
225 type="data" 233 type="data"
226 label="Bed Simple Repeats (Bed4+12) File" 234 label="Bed Simple Repeats (Bed4+12) File"
227 /> 235 />
236 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
228 </when> 237 </when>
229 <when value="bed_splice_junctions_option"> 238 <when value="bed_splice_junctions_option">
230 <param 239 <param
231 format="bed" 240 format="bed"
232 name="BED_splice_junctions" 241 name="BED_splice_junctions"
233 type="data" 242 type="data"
234 label="Bed Splice Junctions (Bed12+1) File" 243 label="Bed Splice Junctions (Bed12+1) File"
235 /> 244 />
245 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
236 </when> 246 </when>
237 <when value="bed_blast_alignment_option"> 247 <when value="bed_blast_alignment_option">
238 <param 248 <param
239 format="bed" 249 format="bed"
240 name="BED_blast_alignment" 250 name="BED_blast_alignment"
241 type="data" 251 type="data"
242 label="Bed Blast Alignments (Bed12+12) File" 252 label="Bed Blast Alignments (Bed12+12) File"
243 /> 253 />
254 <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
244 </when> 255 </when>
245 <when value="bed_blat_alignment_option"> 256 <when value="bed_blat_alignment_option">
246 <param 257 <param
247 format="bed" 258 format="bed"
248 name="BED_blat_alignment" 259 name="BED_blat_alignment"
249 type="data" 260 type="data"
250 label="Bed BLAT Alignments (bigPsl) File" 261 label="Bed BLAT Alignments (bigPsl) File"
251 /> 262 />
263 <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
252 </when> 264 </when>
253 </conditional> 265 </conditional>
254 <param name="longLabel" type="text" size="30" label="Track label" /> 266 <param name="longLabel" type="text" size="30" label="Track label" />
255 <param name="track_color" type="color" label="Track color" value="#000000"> 267 <param name="track_color" type="color" label="Track color" value="#000000">
256 <sanitizer> 268 <sanitizer>
273 <valid initial="string.letters,string.digits"> 285 <valid initial="string.letters,string.digits">
274 <add value="#"/> 286 <add value="#"/>
275 </valid> 287 </valid>
276 </sanitizer> 288 </sanitizer>
277 </param> 289 </param>
290 <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
278 </when> 291 </when>
279 <when value="bigwig"> 292 <when value="bigwig">
280 <param 293 <param
281 format="bigwig" 294 format="bigwig"
282 name="BIGWIG" 295 name="BIGWIG"
289 <valid initial="string.letters,string.digits"> 302 <valid initial="string.letters,string.digits">
290 <add value="#"/> 303 <add value="#"/>
291 </valid> 304 </valid>
292 </sanitizer> 305 </sanitizer>
293 </param> 306 </param>
307 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
294 </when> 308 </when>
295 <when value="gff3"> 309 <when value="gff3">
296 <param 310 <param
297 format="gff3" 311 format="gff3"
298 name="GFF3" 312 name="GFF3"
305 <valid initial="string.letters,string.digits"> 319 <valid initial="string.letters,string.digits">
306 <add value="#"/> 320 <add value="#"/>
307 </valid> 321 </valid>
308 </sanitizer> 322 </sanitizer>
309 </param> 323 </param>
324 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
310 </when> 325 </when>
311 <when value="gtf"> 326 <when value="gtf">
312 <param 327 <param
313 format="gtf" 328 format="gtf"
314 name="GTF" 329 name="GTF"
321 <valid initial="string.letters,string.digits"> 336 <valid initial="string.letters,string.digits">
322 <add value="#"/> 337 <add value="#"/>
323 </valid> 338 </valid>
324 </sanitizer> 339 </sanitizer>
325 </param> 340 </param>
326 </when> 341 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
342 </when>
327 </conditional> 343 </conditional>
328 </repeat> 344 </repeat>
329 </repeat> 345 </repeat>
330 <conditional name="advanced_options"> 346 <conditional name="advanced_options">
331 <param name="advanced_options_selector" type="select" label="Advanced options"> 347 <param name="advanced_options_selector" type="select" label="Advanced options">