Mercurial > repos > yating-l > jbrowsearchivecreator
comparison jbrowseArchiveCreator.xml @ 50:804e7217f27c draft default tip
planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit 3afab1eb0da4823419945c523a1d37cd5973e7f6-dirty
| author | yating-l |
|---|---|
| date | Fri, 20 Jul 2018 11:38:01 -0400 |
| parents | be34d213ec6a |
| children |
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| 49:be34d213ec6a | 50:804e7217f27c |
|---|---|
| 1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.0"> | 1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.2"> |
| 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> |
| 197 format="bam" | 197 format="bam" |
| 198 name="BAM" | 198 name="BAM" |
| 199 type="data" | 199 type="data" |
| 200 label="BAM File" | 200 label="BAM File" |
| 201 /> | 201 /> |
| 202 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> | |
| 202 <param name="longLabel" type="text" size="30" value = "Sequence Alignment" label="Track label" /> | 203 <param name="longLabel" type="text" size="30" value = "Sequence Alignment" label="Track label" /> |
| 203 <param name="track_color" type="color" label="Track color" value="#000000"> | 204 <param name="track_color" type="color" label="Track color" value="#000000"> |
| 204 <sanitizer> | 205 <sanitizer> |
| 205 <valid initial="string.letters,string.digits"> | 206 <valid initial="string.letters,string.digits"> |
| 206 <add value="#"/> | 207 <add value="#"/> |
| 207 </valid> | 208 </valid> |
| 208 </sanitizer> | 209 </sanitizer> |
| 209 </param> | 210 </param> |
| 210 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> | |
| 211 </when> | 211 </when> |
| 212 <when value="bed"> | 212 <when value="bed"> |
| 213 <conditional name="bedChoice"> | 213 <conditional name="bedChoice"> |
| 214 <param name="bed_select" type="select" label="Bed Choice"> | 214 <param name="bed_select" type="select" label="Bed Choice"> |
| 215 <option value="bed_generic">BED Generic</option> | 215 <option value="bed_generic">BED Generic</option> |
| 294 <option value="NCBI" selected="true">NCBI</option> | 294 <option value="NCBI" selected="true">NCBI</option> |
| 295 <option value="UniProt">UniProt</option> | 295 <option value="UniProt">UniProt</option> |
| 296 <option value="FlyBase">FlyBase</option> | 296 <option value="FlyBase">FlyBase</option> |
| 297 <option value="Others">Others</option> | 297 <option value="Others">Others</option> |
| 298 </param> | 298 </param> |
| 299 <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" /> | |
| 299 <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" /> | 300 <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" /> |
| 300 <param name="track_color" type="color" label="Track color" value="#000000"> | 301 <param name="track_color" type="color" label="Track color" value="#000000"> |
| 301 <sanitizer> | 302 <sanitizer> |
| 302 <valid initial="string.letters,string.digits"> | 303 <valid initial="string.letters,string.digits"> |
| 303 <add value="#"/> | 304 <add value="#"/> |
| 304 </valid> | 305 </valid> |
| 305 </sanitizer> | 306 </sanitizer> |
| 306 </param> | 307 </param> |
| 307 <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" /> | |
| 308 </when> | 308 </when> |
| 309 <when value="bigwig"> | 309 <when value="bigwig"> |
| 310 <param | 310 <param |
| 311 format="bigwig" | 311 format="bigwig" |
| 312 name="BIGWIG" | 312 name="BIGWIG" |
| 313 type="data" | 313 type="data" |
| 314 label="BIGWIG File" | 314 label="BIGWIG File" |
| 315 /> | 315 /> |
| 316 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> | |
| 316 <param name="longLabel" type="text" size="30" value="Sequence Coverage" label="Track label" /> | 317 <param name="longLabel" type="text" size="30" value="Sequence Coverage" label="Track label" /> |
| 317 <param name="track_color" type="color" label="Track color" value="#000000"> | 318 <param name="track_color" type="color" label="Track color" value="#000000"> |
| 318 <sanitizer> | 319 <sanitizer> |
| 319 <valid initial="string.letters,string.digits"> | 320 <valid initial="string.letters,string.digits"> |
| 320 <add value="#"/> | 321 <add value="#"/> |
| 321 </valid> | 322 </valid> |
| 322 </sanitizer> | 323 </sanitizer> |
| 323 </param> | 324 </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" /> | |
| 325 </when> | 325 </when> |
| 326 <when value="gff3"> | 326 <when value="gff3"> |
| 327 <param | 327 <param |
| 328 format="gff3" | 328 format="gff3" |
| 329 name="GFF3" | 329 name="GFF3" |
| 330 type="data" | 330 type="data" |
| 331 label="GFF3 File" | 331 label="GFF3 File" |
| 332 /> | 332 /> |
| 333 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> | |
| 333 <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" /> | 334 <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" /> |
| 334 <param name="track_color" type="color" label="Track color" value="#000000"> | 335 <param name="track_color" type="color" label="Track color" value="#000000"> |
| 335 <sanitizer> | 336 <sanitizer> |
| 336 <valid initial="string.letters,string.digits"> | 337 <valid initial="string.letters,string.digits"> |
| 337 <add value="#"/> | 338 <add value="#"/> |
| 338 </valid> | 339 </valid> |
| 339 </sanitizer> | 340 </sanitizer> |
| 340 </param> | 341 </param> |
| 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> | 342 </when> |
| 343 <when value="gtf"> | 343 <when value="gtf"> |
| 344 <param | 344 <param |
| 345 format="gtf" | 345 format="gtf" |
| 346 name="GTF" | 346 name="GTF" |
| 347 type="data" | 347 type="data" |
| 348 label="GTF File" | 348 label="GTF File" |
| 349 /> | 349 /> |
| 350 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> | |
| 350 <param name="longLabel" type="text" size="30" value="Assembled Transcripts" label="Track name" /> | 351 <param name="longLabel" type="text" size="30" value="Assembled Transcripts" label="Track name" /> |
| 351 <param name="track_color" type="color" label="Track color" value="#000000"> | 352 <param name="track_color" type="color" label="Track color" value="#000000"> |
| 352 <sanitizer> | 353 <sanitizer> |
| 353 <valid initial="string.letters,string.digits"> | 354 <valid initial="string.letters,string.digits"> |
| 354 <add value="#"/> | 355 <add value="#"/> |
| 355 </valid> | 356 </valid> |
| 356 </sanitizer> | 357 </sanitizer> |
| 357 </param> | 358 </param> |
| 358 <param name="nameIndex" type="boolean" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> | |
| 359 </when> | 359 </when> |
| 360 </conditional> | 360 </conditional> |
| 361 </repeat> | 361 </repeat> |
| 362 </repeat> | 362 </repeat> |
| 363 <conditional name="advanced_options"> | 363 <conditional name="advanced_options"> |