Mercurial > repos > rmarenco > hubarchivecreator
comparison hubArchiveCreator.xml @ 23:2677f1899aa8 draft
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 |
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| 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> |