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comparison hubArchiveCreator.xml @ 24:fcc1021bd496 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 93e2e2fb59f99677425104a80c17f665fa7b2b4a-dirty
author yating-l
date Wed, 31 May 2017 11:35:16 -0400
parents 2677f1899aa8
children df42241d3731
comparison
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23:2677f1899aa8 24:fcc1021bd496
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
7 <requirements> 7 <requirements>
8 <requirement type="package" version="1.0">ucsc_tools_340</requirement> 8 <requirement type="package" version="340">ucsc_hac</requirement>
9 <requirement type="package" version="1.2">samtools</requirement> 9 <requirement type="package" version="1.2">samtools</requirement>
10 <requirement type="package" version="340">ucsc_bigwig</requirement>
11 <requirement type="package" version="340">ucsc_bigbed</requirement>
10 </requirements> 12 </requirements>
11 13
12 <stdio> 14 <stdio>
13 <regex match="^pass1" 15 <regex match="^pass1"
14 source="stderr" 16 source="stderr"
86 #end if 88 #end if
87 #if $f.formatChoice.format_select == "bed" 89 #if $f.formatChoice.format_select == "bed"
88 #if $f.formatChoice.bedChoice.bed_select == "bed_generic" 90 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
89 --bed $f.formatChoice.bedChoice.BED 91 --bed $f.formatChoice.bedChoice.BED
90 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final, 92 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final,
93 extra_data_dict)
94 #end if
95 #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand"
96 --cytoBand $f.formatChoice.bedChoice.BED_cytoBand
97 #silent $prepare_json($f.formatChoice.bedChoice.BED_cytoBand, $index_track_final,
91 extra_data_dict) 98 extra_data_dict)
92 #end if 99 #end if
93 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" 100 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
94 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats 101 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
95 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, 102 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
100 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, 107 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
101 extra_data_dict) 108 extra_data_dict)
102 #end if 109 #end if
103 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" 110 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
104 --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment 111 --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment
105 #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, 112 #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
106 extra_data_dict) 113 extra_data_dict)
107 #end if 114 #end if
108 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" 115 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
109 --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment 116 --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment
110 #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, 117 #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
111 extra_data_dict) 118 extra_data_dict)
112 #end if 119 #end if
113 #end if 120 #end if
114 #if $f.formatChoice.format_select == "psl" 121 #if $f.formatChoice.format_select == "psl"
115 --psl $f.formatChoice.PSL 122 --psl $f.formatChoice.PSL
117 extra_data_dict) 124 extra_data_dict)
118 #end if 125 #end if
119 #if $f.formatChoice.format_select == "bigwig" 126 #if $f.formatChoice.format_select == "bigwig"
120 --bigwig $f.formatChoice.BIGWIG 127 --bigwig $f.formatChoice.BIGWIG
121 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final, 128 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final,
129 extra_data_dict)
130 #end if
131 #if $f.formatChoice.format_select == "bigbed"
132 --bigbed $f.formatChoice.BIGBED
133 #silent $prepare_json($f.formatChoice.BIGBED, $index_track_final,
122 extra_data_dict) 134 extra_data_dict)
123 #end if 135 #end if
124 #if $f.formatChoice.format_select == "gff3" 136 #if $f.formatChoice.format_select == "gff3"
125 --gff3 $f.formatChoice.GFF3 137 --gff3 $f.formatChoice.GFF3
126 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final, 138 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
178 <param name="format_select" type="select" label="Format"> 190 <param name="format_select" type="select" label="Format">
179 <option value="bam" selected="true">BAM</option> 191 <option value="bam" selected="true">BAM</option>
180 <option value="bed">BED</option> 192 <option value="bed">BED</option>
181 <option value="psl">PSL</option> 193 <option value="psl">PSL</option>
182 <option value="bigwig">BIGWIG</option> 194 <option value="bigwig">BIGWIG</option>
195 <option value="bigbed">BIGBED</option>
183 <option value="gff3">GFF3</option> 196 <option value="gff3">GFF3</option>
184 <option value="gtf">GTF</option> 197 <option value="gtf">GTF</option>
185 </param> 198 </param>
186 199
187 <when value="bam"> 200 <when value="bam">
198 <valid initial="string.letters,string.digits"> 211 <valid initial="string.letters,string.digits">
199 <add value="#"/> 212 <add value="#"/>
200 </valid> 213 </valid>
201 </sanitizer> 214 </sanitizer>
202 </param> 215 </param>
203 </when> 216 </when>
204 <when value="bed"> 217 <when value="bed">
205 <conditional name="bedChoice"> 218 <conditional name="bedChoice">
206 <param name="bed_select" type="select" label="Bed Choice"> 219 <param name="bed_select" type="select" label="Bed Choice">
207 <option value="bed_generic" selected="true">BED Generic (bed3+)</option> 220 <option value="bed_generic" selected="true">BED Generic (bed3+)</option>
221 <option value="bed_cytoBand">cytoBand Track (bed4)</option>
208 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> 222 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
209 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> 223 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
210 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option> 224 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
211 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option> 225 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
212 </param> 226 </param>
216 name="BED" 230 name="BED"
217 type="data" 231 type="data"
218 label="Generic Bed File Choice" 232 label="Generic Bed File Choice"
219 /> 233 />
220 234
235 </when>
236 <when value="bed_cytoBand">
237 <param
238 format="bed"
239 name="BED_cytoBand"
240 type="data"
241 label="cytoBand Track (Bed4)"
242 />
221 </when> 243 </when>
222 <when value="bed_simple_repeats_option"> 244 <when value="bed_simple_repeats_option">
223 <param 245 <param
224 format="bed" 246 format="bed"
225 name="BED_simple_repeats" 247 name="BED_simple_repeats"
291 <add value="#"/> 313 <add value="#"/>
292 </valid> 314 </valid>
293 </sanitizer> 315 </sanitizer>
294 </param> 316 </param>
295 </when> 317 </when>
318 <when value="bigbed">
319 <param
320 format="bigbed"
321 name="BIGBED"
322 type="data"
323 label="BIGBED File"
324 />
325 <param name="longLabel" type="text" size="30" label="Track name" />
326 <param name="track_color" type="color" label="Track color" value="#000000">
327 <sanitizer>
328 <valid initial="string.letters,string.digits">
329 <add value="#"/>
330 </valid>
331 </sanitizer>
332 </param>
333 </when>
296 <when value="gff3"> 334 <when value="gff3">
297 <param 335 <param
298 format="gff3" 336 format="gff3"
299 name="GFF3" 337 name="GFF3"
300 type="data" 338 type="data"
472 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" 510 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
473 compare="sim_size" 511 compare="sim_size"
474 /> 512 />
475 </output> 513 </output>
476 </test> 514 </test>
477 515
478 516
479 <!-- Test with Psl --> 517 <!-- Test with Psl -->
480 <test> 518 <test>
481 <param name="genome_name" value="Dbia3"/> 519 <param name="genome_name" value="Dbia3"/>
482 <param name="fasta_file" value="common/dbia3.fa"/> 520 <param name="fasta_file" value="common/dbia3.fa"/>
1027 1065
1028 <help> 1066 <help>
1029 This Galaxy tool permits to prepare your files to be ready for 1067 This Galaxy tool permits to prepare your files to be ready for
1030 Assembly Hub visualization. 1068 Assembly Hub visualization.
1031 </help> 1069 </help>
1070
1071 <citations>
1072 <citation type="doi">10.7490/f1000research.1112719.1</citation>
1073 </citations>
1032 </tool> 1074 </tool>