Mercurial > repos > rmarenco > hubarchivecreator

comparison hubArchiveCreator.xml @ 26:df42241d3731 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit c11beb58525fe6453a2180fe7783f6e8b0151901-dirty
author yating-l
date Mon, 03 Jul 2017 17:30:20 -0400
parents fcc1021bd496
children cdd33c5c8ac1
comparison
equal deleted inserted replaced
25:99dad5f9444c 26:df42241d3731
71 71
72 ## For each format, we have a few mandatory fields we store in a dict 72 ## For each format, we have a few mandatory fields we store in a dict
73 #set track_color = str($f.formatChoice.track_color) 73 #set track_color = str($f.formatChoice.track_color)
74 #set group_name = str($g.group_name) 74 #set group_name = str($g.group_name)
75 #set longLabel = str($f.formatChoice.longLabel) 75 #set longLabel = str($f.formatChoice.longLabel)
76 #set extra_data_dict = {"track_color": $track_color, 76 #set extra_data_dict = {"database": "",
77 "track_color": $track_color,
77 "group_name": $group_name, 78 "group_name": $group_name,
78 "long_label": $longLabel} 79 "long_label": $longLabel}
79 80
80 #if $f.formatChoice.format_select == "bam" 81 #if $f.formatChoice.format_select == "bam"
81 --bam $f.formatChoice.BAM 82 --bam $f.formatChoice.BAM
107 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, 108 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
108 extra_data_dict) 109 extra_data_dict)
109 #end if 110 #end if
110 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" 111 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
111 --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment 112 --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
113 #set database = str($f.formatChoice.bedChoice.database)
114 #silent extra_data_dict.update({"database": $database})
112 #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, 115 #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
113 extra_data_dict) 116 extra_data_dict)
114 #end if 117 #end if
115 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" 118 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
116 --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment 119 --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment
120 #set database = str($f.formatChoice.bedChoice.database)
121 #silent extra_data_dict.update({"database": $database})
117 #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, 122 #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
118 extra_data_dict) 123 extra_data_dict)
119 #end if 124 #end if
120 #end if 125 #end if
121 #if $f.formatChoice.format_select == "psl" 126 #if $f.formatChoice.format_select == "psl"
202 format="bam" 207 format="bam"
203 name="BAM" 208 name="BAM"
204 type="data" 209 type="data"
205 label="BAM File" 210 label="BAM File"
206 /> 211 />
207 <param name="longLabel" type="text" size="80" label="Track label" /> 212 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
208 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others --> 213 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
209 <param name="track_color" type="color" label="Track color" value="#000000"> 214 <param name="track_color" type="color" label="Track color" value="#000000">
210 <sanitizer> 215 <sanitizer>
211 <valid initial="string.letters,string.digits"> 216 <valid initial="string.letters,string.digits">
212 <add value="#"/> 217 <add value="#"/>
262 format="bed" 267 format="bed"
263 name="BED_blast_alignment" 268 name="BED_blast_alignment"
264 type="data" 269 type="data"
265 label="Bed Blast Alignments (Bed12+12) File" 270 label="Bed Blast Alignments (Bed12+12) File"
266 /> 271 />
272 <param name="database" type="select" label="Protein database">
273 <option value="NCBI" selected="true">NCBI</option>
274 <option value="UniProt">UniProt</option>
275 <option value="FlyBase">FlyBase</option>
276 <option value="Others">Others</option>
277 </param>
267 </when> 278 </when>
268 <when value="bed_blat_alignment_option"> 279 <when value="bed_blat_alignment_option">
269 <param 280 <param
270 format="bed" 281 format="bed"
271 name="BED_blat_alignment" 282 name="BED_blat_alignment"
272 type="data" 283 type="data"
273 label="Bed BLAT Alignments (bigPsl) File" 284 label="Bed BLAT Alignments (bigPsl) File"
274 /> 285 />
286 <param name="database" type="select" label="mRNA database">
287 <option value="NCBI" selected="true">NCBI</option>
288 <option value="Others">Others</option>
289 </param>
275 </when> 290 </when>
276 </conditional> 291 </conditional>
277 <param name="longLabel" type="text" size="30" label="Track name" /> 292 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
278 <param name="track_color" type="color" label="Track color" value="#000000"> 293 <param name="track_color" type="color" label="Track color" value="#000000">
279 <sanitizer> 294 <sanitizer>
280 <valid initial="string.letters,string.digits"> 295 <valid initial="string.letters,string.digits">
281 <add value="#"/> 296 <add value="#"/>
282 </valid> 297 </valid>
288 format="psl" 303 format="psl"
289 name="PSL" 304 name="PSL"
290 type="data" 305 type="data"
291 label="PSL File" 306 label="PSL File"
292 /> 307 />
293 <param name="longLabel" type="text" size="30" label="Track name" /> 308 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
294 <param name="track_color" type="color" label="Track color" value="#000000"> 309 <param name="track_color" type="color" label="Track color" value="#000000">
295 <sanitizer> 310 <sanitizer>
296 <valid initial="string.letters,string.digits"> 311 <valid initial="string.letters,string.digits">
297 <add value="#"/> 312 <add value="#"/>
298 </valid> 313 </valid>
304 format="bigwig" 319 format="bigwig"
305 name="BIGWIG" 320 name="BIGWIG"
306 type="data" 321 type="data"
307 label="BIGWIG File" 322 label="BIGWIG File"
308 /> 323 />
309 <param name="longLabel" type="text" size="30" label="Track name" /> 324 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
310 <param name="track_color" type="color" label="Track color" value="#000000"> 325 <param name="track_color" type="color" label="Track color" value="#000000">
311 <sanitizer> 326 <sanitizer>
312 <valid initial="string.letters,string.digits"> 327 <valid initial="string.letters,string.digits">
313 <add value="#"/> 328 <add value="#"/>
314 </valid> 329 </valid>
320 format="bigbed" 335 format="bigbed"
321 name="BIGBED" 336 name="BIGBED"
322 type="data" 337 type="data"
323 label="BIGBED File" 338 label="BIGBED File"
324 /> 339 />
325 <param name="longLabel" type="text" size="30" label="Track name" /> 340 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
326 <param name="track_color" type="color" label="Track color" value="#000000"> 341 <param name="track_color" type="color" label="Track color" value="#000000">
327 <sanitizer> 342 <sanitizer>
328 <valid initial="string.letters,string.digits"> 343 <valid initial="string.letters,string.digits">
329 <add value="#"/> 344 <add value="#"/>
330 </valid> 345 </valid>
336 format="gff3" 351 format="gff3"
337 name="GFF3" 352 name="GFF3"
338 type="data" 353 type="data"
339 label="GFF3 File" 354 label="GFF3 File"
340 /> 355 />
341 <param name="longLabel" type="text" size="30" label="Track name" /> 356 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
342 <param name="track_color" type="color" label="Track color" value="#000000"> 357 <param name="track_color" type="color" label="Track color" value="#000000">
343 <sanitizer> 358 <sanitizer>
344 <valid initial="string.letters,string.digits"> 359 <valid initial="string.letters,string.digits">
345 <add value="#"/> 360 <add value="#"/>
346 </valid> 361 </valid>
352 format="gtf" 367 format="gtf"
353 name="GTF" 368 name="GTF"
354 type="data" 369 type="data"
355 label="GTF File" 370 label="GTF File"
356 /> 371 />
357 <param name="longLabel" type="text" size="30" label="Track name" /> 372 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
358 <param name="track_color" type="color" label="Track color" value="#000000"> 373 <param name="track_color" type="color" label="Track color" value="#000000">
359 <sanitizer> 374 <sanitizer>
360 <valid initial="string.letters,string.digits"> 375 <valid initial="string.letters,string.digits">
361 <add value="#"/> 376 <add value="#"/>
362 </valid> 377 </valid>