Mercurial > repos > rmarenco > hubarchivecreator

comparison hubArchiveCreator.xml @ 21:884ee2a71680 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 6ac76e7da539ca1773fb809054679f0bf8a06972-dirty
author yating-l
date Wed, 12 Apr 2017 15:05:33 -0400
parents 40469b265ddb
children 7ddf651457df
comparison
equal deleted inserted replaced
20:40469b265ddb 21:884ee2a71680
1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.0"> 1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.3.1">
2 <description> 2 <description>
3 This Galaxy tool permits to prepare your files to be ready for 3 This Galaxy tool permits to prepare your files to be ready for
4 Assembly Hub visualization. 4 Assembly Hub visualization.
5 </description> 5 </description>
6 6
97 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option" 97 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
98 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions 98 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
99 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, 99 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
100 extra_data_dict) 100 extra_data_dict)
101 #end if 101 #end if
102 #if $f.formatChoice.bedChoice.bed_select == "bigpsl_option" 102 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
103 --bigpsl $f.formatChoice.bedChoice.bigPsl 103 --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
104 #silent $prepare_json($f.formatChoice.bedChoice.bigPsl, $index_track_final, 104 #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
105 extra_data_dict) 105 extra_data_dict)
106 #end if 106 #end if
107 #end if 107 #end if
108 #if $f.formatChoice.format_select == "psl" 108 #if $f.formatChoice.format_select == "psl"
109 --psl $f.formatChoice.PSL 109 --psl $f.formatChoice.PSL
110 #silent $prepare_json($f.formatChoice.PSL, $index_track_final, 110 #silent $prepare_json($f.formatChoice.PSL, $index_track_final,
123 #if $f.formatChoice.format_select == "gtf" 123 #if $f.formatChoice.format_select == "gtf"
124 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 124 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
125 --gtf $f.formatChoice.GTF 125 --gtf $f.formatChoice.GTF
126 #silent $prepare_json($f.formatChoice.GTF, $index_track_final, 126 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
127 extra_data_dict) 127 extra_data_dict)
128 #end if
129 #if $f.formatChoice.format_select == "bigpsl"
130 --bigpsl $f.formatChoice.BIGPSL
131 #silent $prepare_json($f.formatChoice.BIGPSL, $index_track_final,
132 extra_data_dict)
128 #end if 133 #end if
129 #end for 134 #end for
130 #end for 135 #end for
131 136
132 ## We combine the fasta file dataset name with his false path in a JSON object 137 ## We combine the fasta file dataset name with his false path in a JSON object
174 <option value="bed">BED</option> 179 <option value="bed">BED</option>
175 <option value="psl">PSL</option> 180 <option value="psl">PSL</option>
176 <option value="bigwig">BIGWIG</option> 181 <option value="bigwig">BIGWIG</option>
177 <option value="gff3">GFF3</option> 182 <option value="gff3">GFF3</option>
178 <option value="gtf">GTF</option> 183 <option value="gtf">GTF</option>
184 <option value="bigpsl">BigPsl</option>
179 </param> 185 </param>
180 186
181 <when value="bam"> 187 <when value="bam">
182 <param 188 <param
183 format="bam" 189 format="bam"
191 <valid initial="string.letters,string.digits"> 197 <valid initial="string.letters,string.digits">
192 <add value="#"/> 198 <add value="#"/>
193 </valid> 199 </valid>
194 </sanitizer> 200 </sanitizer>
195 </param> 201 </param>
196 </when> 202 </when>
197 <when value="bed"> 203 <when value="bed">
198 <conditional name="bedChoice"> 204 <conditional name="bedChoice">
199 <param name="bed_select" type="select" label="Bed Choice"> 205 <param name="bed_select" type="select" label="Bed Choice">
200 <option value="bed_generic" selected="true">BED Generic (bed3+)</option> 206 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
201 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> 207 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
202 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> 208 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
203 <option value="bigpsl_option">bigPsl (bed12+12 / bigPsl.as)</option> 209 <option value="bed_blast_alignment_option">BED Blast alignments (bed12+12 / bigPsl.as)</option>
204 </param> 210 </param>
205 <when value="bed_generic"> 211 <when value="bed_generic">
206 <param 212 <param
207 format="bed" 213 format="bed"
208 name="BED" 214 name="BED"
225 name="BED_splice_junctions" 231 name="BED_splice_junctions"
226 type="data" 232 type="data"
227 label="Bed Splice Junctions (Bed12+1) File" 233 label="Bed Splice Junctions (Bed12+1) File"
228 /> 234 />
229 </when> 235 </when>
230 <when value="bigpsl_option"> 236 <when value="bed_blast_alignment_option">
231 <param 237 <param
232 format="bed" 238 format="bed"
233 name="bigPsl" 239 name="BED_blast_alignment"
234 type="data" 240 type="data"
235 label="bigPsl (Bed12+12) File" 241 label="Bed Blast Alignments (Bed12+12) File"
236 /> 242 />
237 </when> 243 </when>
238 </conditional> 244 </conditional>
239 <param name="track_color" type="color" label="Track color" value="#000000"> 245 <param name="track_color" type="color" label="Track color" value="#000000">
240 <sanitizer> 246 <sanitizer>
302 <add value="#"/> 308 <add value="#"/>
303 </valid> 309 </valid>
304 </sanitizer> 310 </sanitizer>
305 </param> 311 </param>
306 </when> 312 </when>
313 <when value="bigpsl">
314 <param
315 format="bigpsl"
316 name="BIGPSL"
317 type="data"
318 label="bigPsl File"
319 />
320 <param name="track_color" type="color" label="Track color" value="#000000">
321 <sanitizer>
322 <valid initial="string.letters,string.digits">
323 <add value="#"/>
324 </valid>
325 </sanitizer>
326 </param>
327 </when>
307 </conditional> 328 </conditional>
308 </repeat> 329 </repeat>
309 </repeat> 330 </repeat>
310 <conditional name="advanced_options"> 331 <conditional name="advanced_options">
311 <param name="advanced_options_selector" type="select" label="Advanced options"> 332 <param name="advanced_options_selector" type="select" label="Advanced options">