Mercurial > repos > yating-l > hubarchivecreator
comparison hubArchiveCreator.xml @ 6:2cc7685a7182 draft
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 48b59e91e2dcc2e97735ee35d587960cbfbce932
| author | yating-l |
|---|---|
| date | Wed, 21 Dec 2016 18:00:09 -0500 |
| parents | 7b0d359de7ee |
| children | dd1e233e16a1 |
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| 5:7b0d359de7ee | 6:2cc7685a7182 |
|---|---|
| 107 extra_data_dict) | 107 extra_data_dict) |
| 108 #end if | 108 #end if |
| 109 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" | 109 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" |
| 110 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats | 110 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats |
| 111 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, | 111 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, |
| 112 extra_data_dict) | |
| 113 #end if | |
| 114 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option" | |
| 115 --bedSpliceJunctions $f.formatChoice.bedChoice.Bed_splice_junctions | |
| 116 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, | |
| 112 extra_data_dict) | 117 extra_data_dict) |
| 113 #end if | 118 #end if |
| 114 #end if | 119 #end if |
| 115 #if $f.formatChoice.format_select == "psl" | 120 #if $f.formatChoice.format_select == "psl" |
| 116 --psl $f.formatChoice.PSL | 121 --psl $f.formatChoice.PSL |
| 204 <when value="bed"> | 209 <when value="bed"> |
| 205 <conditional name="bedChoice"> | 210 <conditional name="bedChoice"> |
| 206 <param name="bed_select" type="select" label="Bed Choice"> | 211 <param name="bed_select" type="select" label="Bed Choice"> |
| 207 <option value="bed_generic" selected="true">BED Generic (bed3+)</option> | 212 <option value="bed_generic" selected="true">BED Generic (bed3+)</option> |
| 208 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> | 213 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> |
| 214 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> | |
| 209 </param> | 215 </param> |
| 210 <when value="bed_generic"> | 216 <when value="bed_generic"> |
| 211 <param | 217 <param |
| 212 format="bed" | 218 format="bed" |
| 213 name="BED" | 219 name="BED" |
| 220 <param | 226 <param |
| 221 format="bed" | 227 format="bed" |
| 222 name="BED_simple_repeats" | 228 name="BED_simple_repeats" |
| 223 type="data" | 229 type="data" |
| 224 label="Bed Simple Repeats (Bed4+12) File" | 230 label="Bed Simple Repeats (Bed4+12) File" |
| 231 /> | |
| 232 </when> | |
| 233 <when value="bed_splice_junctions_option"> | |
| 234 <param | |
| 235 format="bed" | |
| 236 name="BED_splice_junctions" | |
| 237 type="data" | |
| 238 label="Bed Splice Junctions (Bed12+1) File" | |
| 225 /> | 239 /> |
| 226 </when> | 240 </when> |
| 227 </conditional> | 241 </conditional> |
| 228 <param name="track_color" type="color" label="Track color" value="#000000"> | 242 <param name="track_color" type="color" label="Track color" value="#000000"> |
| 229 <sanitizer> | 243 <sanitizer> |
| 440 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" | 454 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" |
| 441 compare="sim_size" | 455 compare="sim_size" |
| 442 /> | 456 /> |
| 443 </output> | 457 </output> |
| 444 </test> | 458 </test> |
| 459 | |
| 445 | 460 |
| 446 <!-- Test with Psl --> | 461 <!-- Test with Psl --> |
| 447 <test> | 462 <test> |
| 448 <param name="genome_name" value="Dbia3"/> | 463 <param name="genome_name" value="Dbia3"/> |
| 449 <param name="fasta_file" value="common/dbia3.fa"/> | 464 <param name="fasta_file" value="common/dbia3.fa"/> |