Mercurial > repos > rmarenco > hubarchivecreator

comparison hubArchiveCreator.xml @ 23:2677f1899aa8 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 07210e24fe7d22f5dfc84061310280f67f781fb1-dirty
author yating-l
date Tue, 09 May 2017 15:42:43 -0400
parents 7ddf651457df
children fcc1021bd496
comparison
equal deleted inserted replaced
22:7ddf651457df 23:2677f1899aa8
68 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track) 68 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
69 69
70 ## For each format, we have a few mandatory fields we store in a dict 70 ## For each format, we have a few mandatory fields we store in a dict
71 #set track_color = str($f.formatChoice.track_color) 71 #set track_color = str($f.formatChoice.track_color)
72 #set group_name = str($g.group_name) 72 #set group_name = str($g.group_name)
73 73 #set longLabel = str($f.formatChoice.longLabel)
74 #set extra_data_dict = {"track_color": $track_color, 74 #set extra_data_dict = {"track_color": $track_color,
75 "group_name": $group_name} 75 "group_name": $group_name,
76 "long_label": $longLabel}
76 77
77 #if $f.formatChoice.format_select == "bam" 78 #if $f.formatChoice.format_select == "bam"
78 --bam $f.formatChoice.BAM 79 --bam $f.formatChoice.BAM
79 #set bam_index = $f.formatChoice.BAM.metadata.bam_index 80 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
80 81
188 format="bam" 189 format="bam"
189 name="BAM" 190 name="BAM"
190 type="data" 191 type="data"
191 label="BAM File" 192 label="BAM File"
192 /> 193 />
194 <param name="longLabel" type="text" size="80" label="Track label" />
193 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others --> 195 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
194 <param name="track_color" type="color" label="Track color" value="#000000"> 196 <param name="track_color" type="color" label="Track color" value="#000000">
195 <sanitizer> 197 <sanitizer>
196 <valid initial="string.letters,string.digits"> 198 <valid initial="string.letters,string.digits">
197 <add value="#"/> 199 <add value="#"/>
248 type="data" 250 type="data"
249 label="Bed BLAT Alignments (bigPsl) File" 251 label="Bed BLAT Alignments (bigPsl) File"
250 /> 252 />
251 </when> 253 </when>
252 </conditional> 254 </conditional>
255 <param name="longLabel" type="text" size="30" label="Track name" />
253 <param name="track_color" type="color" label="Track color" value="#000000"> 256 <param name="track_color" type="color" label="Track color" value="#000000">
254 <sanitizer> 257 <sanitizer>
255 <valid initial="string.letters,string.digits"> 258 <valid initial="string.letters,string.digits">
256 <add value="#"/> 259 <add value="#"/>
257 </valid> 260 </valid>
263 format="psl" 266 format="psl"
264 name="PSL" 267 name="PSL"
265 type="data" 268 type="data"
266 label="PSL File" 269 label="PSL File"
267 /> 270 />
271 <param name="longLabel" type="text" size="30" label="Track name" />
268 <param name="track_color" type="color" label="Track color" value="#000000"> 272 <param name="track_color" type="color" label="Track color" value="#000000">
269 <sanitizer> 273 <sanitizer>
270 <valid initial="string.letters,string.digits"> 274 <valid initial="string.letters,string.digits">
271 <add value="#"/> 275 <add value="#"/>
272 </valid> 276 </valid>
278 format="bigwig" 282 format="bigwig"
279 name="BIGWIG" 283 name="BIGWIG"
280 type="data" 284 type="data"
281 label="BIGWIG File" 285 label="BIGWIG File"
282 /> 286 />
287 <param name="longLabel" type="text" size="30" label="Track name" />
283 <param name="track_color" type="color" label="Track color" value="#000000"> 288 <param name="track_color" type="color" label="Track color" value="#000000">
284 <sanitizer> 289 <sanitizer>
285 <valid initial="string.letters,string.digits"> 290 <valid initial="string.letters,string.digits">
286 <add value="#"/> 291 <add value="#"/>
287 </valid> 292 </valid>
293 format="gff3" 298 format="gff3"
294 name="GFF3" 299 name="GFF3"
295 type="data" 300 type="data"
296 label="GFF3 File" 301 label="GFF3 File"
297 /> 302 />
303 <param name="longLabel" type="text" size="30" label="Track name" />
298 <param name="track_color" type="color" label="Track color" value="#000000"> 304 <param name="track_color" type="color" label="Track color" value="#000000">
299 <sanitizer> 305 <sanitizer>
300 <valid initial="string.letters,string.digits"> 306 <valid initial="string.letters,string.digits">
301 <add value="#"/> 307 <add value="#"/>
302 </valid> 308 </valid>
308 format="gtf" 314 format="gtf"
309 name="GTF" 315 name="GTF"
310 type="data" 316 type="data"
311 label="GTF File" 317 label="GTF File"
312 /> 318 />
319 <param name="longLabel" type="text" size="30" label="Track name" />
313 <param name="track_color" type="color" label="Track color" value="#000000"> 320 <param name="track_color" type="color" label="Track color" value="#000000">
314 <sanitizer> 321 <sanitizer>
315 <valid initial="string.letters,string.digits"> 322 <valid initial="string.letters,string.digits">
316 <add value="#"/> 323 <add value="#"/>
317 </valid> 324 </valid>