Mercurial > repos > yating-l > jbrowsearchivecreator

comparison jbrowseArchiveCreator.xml @ 15:6464399df918 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit c69fafd096990eadcc380250703aefd919f80107
author yating-l
date Wed, 20 Jun 2018 17:43:26 -0400
parents 3f9971a91096
children 8bcec8dbb8be
comparison
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14:3f9971a91096 15:6464399df918
1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.0"> 1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.1">
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">