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comparison hubArchiveCreator.xml @ 29:7e8a8b732db3 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Wed, 16 May 2018 18:04:20 -0400
parents 6aa28a85cc38
children e7c4be523cb7
comparison
equal deleted inserted replaced
28:6aa28a85cc38 29:7e8a8b732db3
1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.4.2"> 1 <tool id="hubArchiveCreator" name="Hub Archive Creator" version="2.5.0">
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 <macros>
7 <import>macros.xml</import>
8 </macros>
6 9
7 <requirements> 10 <requirements>
8 <requirement type="package" version="340">ucsc_hac</requirement> 11 <requirement type="package" version="340">ucsc_hac</requirement>
9 <requirement type="package" version="1.2">samtools</requirement> 12 <requirement type="package" version="1.2">samtools</requirement>
10 <requirement type="package" version="340">ucsc_bigwig</requirement> 13 <requirement type="package" version="340">ucsc_bigwig</requirement>
21 </stdio> 24 </stdio>
22 25
23 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] --> 26 <!-- Idea: python \ -augustus [parameters] \ -trfBig [parameters] -->
24 <command detect_errors="exit_code"><![CDATA[ 27 <command detect_errors="exit_code"><![CDATA[
25 mkdir -p $output.extra_files_path; 28 mkdir -p $output.extra_files_path;
26 29
27 python $__tool_directory__/hubArchiveCreator.py 30 ## Dump the tool parameters into a JSON file
28 31 python $json_file parameters.json;
29 ## Ask the user to enter the genome name 32
30 --genome_name '$genome_name' 33 python $__tool_directory__/hubArchiveCreator.py --data_json parameters.json -o $output;
31 34
32 #import json 35
33 36 ]]></command>
34 #set global data_parameter_dict = {} 37 <configfiles>
35 38 <configfile name="json_file">
36 ## Function to retrieve the data of the inputs 39 import json
37 #def prepare_json($input_to_prepare, $order_index, $extra_data_dict={}) 40 import sys
38 #set false_path = str($input_to_prepare) 41
39 #set name = $input_to_prepare.name 42 file_path = sys.argv[1]
40 43 #set global $data_parameter_dict = {}
41 #set data_dict = {"name": $name} 44
42 #silent data_dict.update($extra_data_dict) 45 ## Ask the user to enter the genome name
43 46 #silent $data_parameter_dict.update({"genome_name": str($genome_name)})
44 ## Add the ordering by taking the tool form indexes 47
45 #silent $data_dict.update({"order_index": $order_index}) 48 ## Function to retrieve the data of the inputs
46 49 #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
47 #silent $data_parameter_dict.update({$false_path: $data_dict}) 50 #set false_path = str($input_to_prepare)
48 51 #set $data_dict = {"false_path": $false_path}
49 #end def 52
50 53 #set name = str($input_to_prepare.name)
51 54 #silent $data_dict.update({"name": $name})
52 ## Get the number of digits from tracks, to have a unique integer from group index and track index 55 #silent $data_dict.update($extra_data_dict)
53 56 ## Add the ordering by taking the tool form indexes
54 #set temp_max_digit = 0 57 #silent $data_dict.update({"order_index": $order_index})
55 58
56 #for $g in $group 59 #if $datatype in $data_parameter_dict
57 #if len($g.format) > $temp_max_digit 60 #silent $data_parameter_dict[$datatype].append($data_dict)
58 #silent temp_max_digit = len($g.format) 61 #else
62 #set array_inputs = []
63 #silent $array_inputs.append($data_dict)
64 #silent $data_parameter_dict.update({$datatype: $array_inputs})
65 #end if
66 #end def
67
68 ## Get the number of digits from tracks, to have a unique integer from group index and track index
69
70 #set temp_max_digit = 0
71
72 #for $g in $group
73 #if len($g.format) > $temp_max_digit
74 #silent temp_max_digit = len($g.format)
75 #end if
76 #end for
77
78
79 #set nb_digits_max_track = len(str($temp_max_digit))
80
81 ## END Get the number of digits
82
83 #for $i_g, $g in enumerate( $group )
84 #for $i, $f in enumerate( $g.format )
85 ## Create the order index using index_group+1 concatenated with index_track
86 #set index_group_final = str($i_g + 1)
87 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
88
89 ## For each format, we have a few mandatory fields we store in a dict
90 #set track_color = str($f.formatChoice.track_color)
91 #set group_name = str($g.group_name)
92 #set longLabel = str($f.formatChoice.longLabel)
93 #set extra_data_dict = {"track_color": $track_color,
94 "group_name": $group_name,
95 "long_label": $longLabel}
96
97 #if $f.formatChoice.format_select == "bam"
98 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
99
100 ## Add Bam format specific fields
101 #silent $extra_data_dict.update({"index": $bam_index})
102
103 #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
104 #end if
105 #if $f.formatChoice.format_select == "bed"
106 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
107 #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED, $index_track_final,
108 $extra_data_dict)
59 #end if 109 #end if
60 #end for 110 #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand"
61 111 #silent $prepare_json("CytoBand", $f.formatChoice.bedChoice.BED_cytoBand, $index_track_final,
62 #set nb_digits_max_track = len(str($temp_max_digit)) 112 $extra_data_dict)
63 113 #end if
64 ## END Get the number of digits 114 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
65 115 #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
66 #for $i_g, $g in enumerate( $group ) 116 $extra_data_dict)
67 #for $i, $f in enumerate( $g.format ) 117 #end if
68 ## Create the order index using index_group+1 concatenated with index_track 118 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
69 #set index_group_final = str($i_g + 1) 119 #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
70 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track) 120 $extra_data_dict)
71 121 #end if
72 ## For each format, we have a few mandatory fields we store in a dict 122 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
73 #set track_color = str($f.formatChoice.track_color) 123 #set database = str($f.formatChoice.bedChoice.database)
74 #set group_name = str($g.group_name) 124 #silent $extra_data_dict.update({"database": $database})
75 #set longLabel = str($f.formatChoice.longLabel) 125 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
76 #set extra_data_dict = {"database": "", 126 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
77 "track_color": $track_color, 127 #if $i.element_identifier.endswith("ix")
78 "group_name": $group_name, 128 #$extra_data_dict.update({"index_ix": str($i)})
79 "long_label": $longLabel} 129 #elif $i.element_identifier.endswith("ixx")
80 130 #$extra_data_dict.update({"index_ixx": str($i)})
81 #if $f.formatChoice.format_select == "bam" 131 #end if
82 --bam $f.formatChoice.BAM 132 #end for
83 #set bam_index = $f.formatChoice.BAM.metadata.bam_index 133 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
84 134 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
85 ## Add Bam format specific fields 135 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
86 #silent extra_data_dict.update({"index": $bam_index})
87
88 #silent $prepare_json($f.formatChoice.BAM, $index_track_final, extra_data_dict)
89 #end if 136 #end if
90 #if $f.formatChoice.format_select == "bed" 137 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
91 #if $f.formatChoice.bedChoice.bed_select == "bed_generic" 138 $extra_data_dict)
92 --bed $f.formatChoice.bedChoice.BED 139 #end if
93 #silent $prepare_json($f.formatChoice.bedChoice.BED, $index_track_final, 140 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
94 extra_data_dict) 141 #set database = str($f.formatChoice.bedChoice.database)
142 #silent $extra_data_dict.update({"database": $database})
143 #if $f.formatChoice.bedChoice.add_trix_index.add_trix_index_selector == "yes"
144 #for i in $f.formatChoice.bedChoice.add_trix_index.trix_index
145 #if $i.element_identifier.endswith("ix")
146 #$extra_data_dict.update({"index_ix": str($i)})
147 #elif $i.element_identifier.endswith("ixx")
148 #$extra_data_dict.update({"index_ixx": str($i)})
149 #end if
150 #end for
151 ##set ix_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ix)
152 ##set ixx_index = str($f.formatChoice.bedChoice.add_trix_index.trix_index.index_ixx)
153 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index})
154 #end if
155 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
156 $extra_data_dict)
157 #end if
158 #end if
159 #if $f.formatChoice.format_select == "psl"
160 #silent $prepare_json("Psl", $f.formatChoice.PSL, $index_track_final,
161 $extra_data_dict)
162 #end if
163 #if $f.formatChoice.format_select == "bigwig"
164 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
165 $extra_data_dict)
166 #end if
167 #if $f.formatChoice.format_select == "bigbed"
168 #if $f.formatChoice.add_trix_index.add_trix_index_selector == "yes"
169 ##set ix_index = str($f.formatChoice.add_trix_index.trix_index.index_ix)
170 ##set ixx_index = str($f.formatChoice.add_trix_index.trix_index.index_ixx)
171 #for i in $f.formatChoice.add_trix_index.trix_index
172 #if $i.element_identifier.endswith("ix")
173 #$extra_data_dict.update({"index_ix": str($i)})
174 #elif $i.element_identifier.endswith("ixx")
175 #$extra_data_dict.update({"index_ixx": str($i)})
95 #end if 176 #end if
96 #if $f.formatChoice.bedChoice.bed_select == "bed_cytoBand" 177 #end for
97 --cytoBand $f.formatChoice.bedChoice.BED_cytoBand 178 #$extra_data_dict.update({"trix_id": str($f.formatChoice.add_trix_index.trix_id)})
98 #silent $prepare_json($f.formatChoice.bedChoice.BED_cytoBand, $index_track_final, 179 ##set trix_id = str($f.formatChoice.add_trix_index.trix_id)
99 extra_data_dict) 180 ##silent $extra_data_dict.update({"indexIx": $ix_index, "indexIxx": $ixx_index, "trix_id": $trix_id})
100 #end if 181 #end if
101 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" 182 #silent $prepare_json("BigBed", $f.formatChoice.BIGBED, $index_track_final,
102 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats 183 $extra_data_dict)
103 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final, 184 #end if
104 extra_data_dict) 185 #if $f.formatChoice.format_select == "gff3"
105 #end if 186 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
106 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option" 187 $extra_data_dict)
107 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions 188 #end if
108 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, 189 #if $f.formatChoice.format_select == "gtf"
109 extra_data_dict) 190 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
110 #end if 191 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
111 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" 192 $extra_data_dict)
112 --bedBlastAlignments $f.formatChoice.bedChoice.BED_blast_alignment 193 #end if
113 #set database = str($f.formatChoice.bedChoice.database) 194 #end for
114 #silent extra_data_dict.update({"database": $database}) 195 #end for
115 #silent $prepare_json($f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, 196
116 extra_data_dict) 197 ## We combine the fasta file dataset name with his false path in a JSON object
117 #end if 198 #set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)}
118 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" 199 $data_parameter_dict.update({"fasta": $fasta_json})
119 --bigpsl $f.formatChoice.bedChoice.BED_blat_alignment 200
120 #set database = str($f.formatChoice.bedChoice.database) 201 ## Retrieve the user email
121 #silent extra_data_dict.update({"database": $database}) 202 #silent $data_parameter_dict.update({"user_email": str($__user_email__)})
122 #silent $prepare_json($f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, 203
123 extra_data_dict) 204 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
124 #end if 205
125 #end if 206 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
126 #if $f.formatChoice.format_select == "psl" 207
127 --psl $f.formatChoice.PSL 208 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
128 #silent $prepare_json($f.formatChoice.PSL, $index_track_final, 209
129 extra_data_dict) 210 with open(file_path, 'w') as f:
130 #end if 211 json.dump($data_parameter_dict, f)
131 #if $f.formatChoice.format_select == "bigwig" 212
132 --bigwig $f.formatChoice.BIGWIG 213 </configfile>
133 #silent $prepare_json($f.formatChoice.BIGWIG, $index_track_final, 214 </configfiles>
134 extra_data_dict)
135 #end if
136 #if $f.formatChoice.format_select == "bigbed"
137 --bigbed $f.formatChoice.BIGBED
138 #silent $prepare_json($f.formatChoice.BIGBED, $index_track_final,
139 extra_data_dict)
140 #end if
141 #if $f.formatChoice.format_select == "gff3"
142 --gff3 $f.formatChoice.GFF3
143 #silent $prepare_json($f.formatChoice.GFF3, $index_track_final,
144 extra_data_dict)
145 #end if
146 #if $f.formatChoice.format_select == "gtf"
147 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
148 --gtf $f.formatChoice.GTF
149 #silent $prepare_json($f.formatChoice.GTF, $index_track_final,
150 extra_data_dict)
151 #end if
152 #end for
153 #end for
154
155 ## We combine the fasta file dataset name with his false path in a JSON object
156 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
157 -f '$fasta_json'
158
159 ## Dump the final json
160 #set all_data_json = json.dumps($data_parameter_dict)
161
162 --data_json '$all_data_json'
163
164 ## Retrieve the user email
165 --user_email $__user_email__
166
167 -d $__tool_directory__
168
169 -e $output.extra_files_path
170
171 $advanced_options.debug_mode
172
173 -o $output;
174
175 ]]></command>
176 215
177 <inputs> 216 <inputs>
178 <param 217 <param
179 name="genome_name" 218 name="genome_name"
180 type="text" 219 type="text"
273 <option value="NCBI" selected="true">NCBI</option> 312 <option value="NCBI" selected="true">NCBI</option>
274 <option value="UniProt">UniProt</option> 313 <option value="UniProt">UniProt</option>
275 <option value="FlyBase">FlyBase</option> 314 <option value="FlyBase">FlyBase</option>
276 <option value="Others">Others</option> 315 <option value="Others">Others</option>
277 </param> 316 </param>
317 <expand macro="add_trix_file"/>
278 </when> 318 </when>
279 <when value="bed_blat_alignment_option"> 319 <when value="bed_blat_alignment_option">
280 <param 320 <param
281 format="bed" 321 format="bed"
282 name="BED_blat_alignment" 322 name="BED_blat_alignment"
285 /> 325 />
286 <param name="database" type="select" label="mRNA database"> 326 <param name="database" type="select" label="mRNA database">
287 <option value="NCBI" selected="true">NCBI</option> 327 <option value="NCBI" selected="true">NCBI</option>
288 <option value="Others">Others</option> 328 <option value="Others">Others</option>
289 </param> 329 </param>
330 <expand macro="add_trix_file"/>
290 </when> 331 </when>
291 </conditional> 332 </conditional>
292 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> 333 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
293 <param name="track_color" type="color" label="Track color" value="#000000"> 334 <param name="track_color" type="color" label="Track color" value="#000000">
294 <sanitizer> 335 <sanitizer>
335 format="bigbed" 376 format="bigbed"
336 name="BIGBED" 377 name="BIGBED"
337 type="data" 378 type="data"
338 label="BIGBED File" 379 label="BIGBED File"
339 /> 380 />
381 <expand macro="add_trix_file">
382 <param
383 name="trix_id"
384 value="name"
385 type="text"
386 size="30"
387 label="Specify Trix identifier (The default is name)"
388 />
389 </expand>
340 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" /> 390 <param name="longLabel" type="text" size="76" label="Track label" help="It is limited to 76 printable characters, the first 17 printable characters will be used as a short label of the track" />
341 <param name="track_color" type="color" label="Track color" value="#000000"> 391 <param name="track_color" type="color" label="Track color" value="#000000">
342 <sanitizer> 392 <sanitizer>
343 <valid initial="string.letters,string.digits"> 393 <valid initial="string.letters,string.digits">
344 <add value="#"/> 394 <add value="#"/>
386 <option value="off" selected="true">Hide advanced options</option> 436 <option value="off" selected="true">Hide advanced options</option>
387 <option value="on">Display advanced options</option> 437 <option value="on">Display advanced options</option>
388 </param> 438 </param>
389 <!-- TODO: Avoid redundancy here --> 439 <!-- TODO: Avoid redundancy here -->
390 <when value="on"> 440 <when value="on">
391 <param name="debug_mode" type="boolean" 441 <param name="debug_mode" type="select" label="Activate debug mode">
392 label="Activate debug mode" checked="false" 442 <option value="false" selected="true">No</option>
393 truevalue="--debug_mode" falsevalue=""> 443 <option value="true">Yes</option>
394 <help> 444 <help>
395 Use this option if you are a G-OnRamp developer 445 Use this option if you are a G-OnRamp developer
396 </help> 446 </help>
397 </param> 447 </param>
398 </when> 448 </when>
399 <when value="off"> 449 <when value="off">
400 <param name="debug_mode" type="hidden" 450 <param name="debug_mode" type="hidden"
401 value=""> 451 value="false">
402 </param> 452 </param>
403 </when> 453 </when>
404 </conditional> 454 </conditional>
405 </inputs> 455 </inputs>
406 456
407 <outputs> 457 <outputs>
408 <data format="trackhub" name="output"/> 458 <data format="trackhub" name="output"/>
409 </outputs> 459 </outputs>
410 460
411 <tests> 461 <tests>
412 <!-- Test with only the fasta file --> 462
463 <!-- Test with only the fasta file -->
413 <test> 464 <test>
414 <param name="genome_name" value="Dbia3"/> 465 <param name="genome_name" value="Dbia3"/>
415 <param name="fasta_file" value="common/dbia3.fa"/> 466 <param name="fasta_file" value="common/dbia3.fa"/>
416 <output name="output" file="only_genome/only_genome.html"> 467 <output name="output" file="only_genome/only_genome.html">
417 <extra_files type="file" name="__main__.log" value="only_genome/__main__.log" /> 468 <!-- Use macro to check the whole common structure without repeated code -->
418 <extra_files type="file" name="myHub/genomes.txt" value="only_genome/myHub/genomes.txt" /> 469 <expand macro="verify_hub_structure_no_track" test="only_genome" />
419 <extra_files type="file" name="myHub/Dbia3.html" value="only_genome/myHub/Dbia3.html"/>
420 <!-- Email could be different, but we need to ensure we still have the email line -->
421 <extra_files type="file" name="myHub/hub.txt" value="only_genome/myHub/hub.txt" lines_diff="2">
422 <assert_contents>
423 <has_text text="email"/>
424 </assert_contents>
425 </extra_files>
426 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
427 </extra_files>
428 <extra_files type="file" name="myHub/Dbia3/description.html" value="only_genome/myHub/Dbia3/description.html"/>
429 </output> 470 </output>
430 </test> 471 </test>
431 472
432 <!-- Test with Bam --> 473 <!-- Test with Bam -->
433 <test> 474 <test>
437 <param name="group_name" value="Default group"/> 478 <param name="group_name" value="Default group"/>
438 <repeat name="format"> 479 <repeat name="format">
439 <conditional name="formatChoice"> 480 <conditional name="formatChoice">
440 <param name="format_select" value="bam"/> 481 <param name="format_select" value="bam"/>
441 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" /> 482 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam" />
483 <param name="longLabel" value="HISAT sequence alignment" />
442 <param name="track_color" value="#000000"/> 484 <param name="track_color" value="#000000"/>
443 </conditional> 485 </conditional>
444 </repeat> 486 </repeat>
445 </repeat> 487 </repeat>
446 <output name="output" file="bam/bam.html"> 488 <output name="output" file="bam/bam.html">
453 <extra_files type="file" 495 <extra_files type="file"
454 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" 496 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
455 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai" 497 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam.bai"
456 compare="sim_size" 498 compare="sim_size"
457 /> 499 />
458 <!-- Verify trackDb.txt contains the basic fields for a bam --> 500 <!-- Use macro to check the whole common structure without repeated code -->
459 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="bam/myHub/Dbia3/trackDb.txt"> 501 <expand macro="verify_hub_structure" test="bam" />
460 <assert_contents>
461 <has_text text="track"/>
462 <has_text text="longLabel"/>
463 <has_text text="shortLabel"/>
464 <has_text text="bigDataUrl"/>
465 <has_text text="type"/>
466 <has_text text="visibility"/>
467 <has_text text="thickDrawItem"/>
468 <has_text text="priority"/>
469 <has_text text="color"/>
470 <has_text text="group"/>
471 </assert_contents>
472 </extra_files>
473 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
474 </output> 502 </output>
475 </test> 503 </test>
476 504
477 <!-- Test with Bed Generic --> 505 <!-- Test with Bed Generic -->
478 <test> 506 <test>
484 <conditional name="formatChoice"> 512 <conditional name="formatChoice">
485 <param name="format_select" value="bed" /> 513 <param name="format_select" value="bed" />
486 <conditional name="bedChoice"> 514 <conditional name="bedChoice">
487 <param name="bed_select" value="bed_generic"/> 515 <param name="bed_select" value="bed_generic"/>
488 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/> 516 <param name="BED" ftype="bed" value="bed_generic/inputs/TBLASTN_Alignment_to_proteins"/>
517 <param name="longLabel" value="TBLASTN alignment" />
489 <param name="track_color" value="#000000"/> 518 <param name="track_color" value="#000000"/>
490 </conditional> 519 </conditional>
491 </conditional> 520 </conditional>
492 </repeat> 521 </repeat>
493 </repeat> 522 </repeat>
494 <output name="output" file="bed_generic/bed_generic.html"> 523 <output name="output" file="bed_generic/bed_generic.html">
495 <!-- Verify tracks folder contains bam and bai -->
496 <extra_files type="file" 524 <extra_files type="file"
497 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" 525 name="myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
498 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb" 526 value="bed_generic/myHub/Dbia3/tracks/TBLASTN_Alignment_to_proteins.bb"
499 compare="sim_size" 527 compare="sim_size"
500 /> 528 />
529 <expand macro="verify_hub_structure" test="bed_generic" />
501 </output> 530 </output>
502 </test> 531 </test>
503 532
504 <!-- Test with Bed Simple repeat --> 533 <!-- Test with Bed Simple repeat -->
505 <test> 534 <test>
511 <conditional name="formatChoice"> 540 <conditional name="formatChoice">
512 <param name="format_select" value="bed" /> 541 <param name="format_select" value="bed" />
513 <conditional name="bedChoice"> 542 <conditional name="bedChoice">
514 <param name="bed_select" value="bed_simple_repeats_option"/> 543 <param name="bed_select" value="bed_simple_repeats_option"/>
515 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/> 544 <param name="BED_simple_repeats" ftype="bed" value="bed_simple_repeats/inputs/Repeating_Elements_by_TrfBig"/>
545 <param name="longLabel" value="Simple repeat" />
516 <param name="track_color" value="#000000"/> 546 <param name="track_color" value="#000000"/>
517 </conditional> 547 </conditional>
518 </conditional> 548 </conditional>
519 </repeat> 549 </repeat>
520 </repeat> 550 </repeat>
521 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html"> 551 <output name="output" file="bed_simple_repeats/bed_simple_repeats_trackhub.html">
522 <!-- Verify tracks folder contains bam and bai -->
523 <extra_files type="file" 552 <extra_files type="file"
524 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" 553 name="myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
525 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb" 554 value="bed_simple_repeats/myHub/Dbia3/tracks/Repeating_Elements_by_TrfBig.bb"
526 compare="sim_size" 555 compare="sim_size"
527 /> 556 />
528 </output> 557 <expand macro="verify_hub_structure" test="bed_simple_repeats" />
529 </test> 558 </output>
530 559 </test>
531 560
532 <!-- Test with Psl --> 561 <!-- Test with Psl -->
533 <test> 562 <test>
534 <param name="genome_name" value="Dbia3"/> 563 <param name="genome_name" value="Dbia3"/>
535 <param name="fasta_file" value="common/dbia3.fa"/> 564 <param name="fasta_file" value="common/dbia3.fa"/>
537 <param name="group_name" value="Default group"/> 566 <param name="group_name" value="Default group"/>
538 <repeat name="format"> 567 <repeat name="format">
539 <conditional name="formatChoice"> 568 <conditional name="formatChoice">
540 <param name="format_select" value="psl"/> 569 <param name="format_select" value="psl"/>
541 <param name="PSL" value="psl/inputs/blastXmlToPsl"/> 570 <param name="PSL" value="psl/inputs/blastXmlToPsl"/>
571 <param name="longLabel" value="BLAST Alignment" />
542 <param name="track_color" value="#000000"/> 572 <param name="track_color" value="#000000"/>
543 </conditional> 573 </conditional>
544 </repeat> 574 </repeat>
545 </repeat> 575 </repeat>
546 <output name="output" file="psl/psl_trackhub.html"> 576 <output name="output" file="psl/psl_trackhub.html">
547 <!-- Verify tracks folder contains bam and bai -->
548 <extra_files type="file" 577 <extra_files type="file"
549 name="myHub/Dbia3/tracks/blastXmlToPsl.bb" 578 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
550 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb" 579 value="psl/myHub/Dbia3/tracks/blastXmlToPsl.bb"
551 compare="sim_size" 580 compare="sim_size"
552 /> 581 />
553 <!-- Verify trackDb.txt contains the basic fields for a bam --> 582 <expand macro="verify_hub_structure" test="psl" />
554 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
555 </output> 583 </output>
556 </test> 584 </test>
557 585
558 <!-- Test with BigWig --> 586 <!-- Test with BigWig -->
559 <test> 587 <test>
562 <repeat name="group"> 590 <repeat name="group">
563 <param name="group_name" value="Default group"/> 591 <param name="group_name" value="Default group"/>
564 <repeat name="format"> 592 <repeat name="format">
565 <conditional name="formatChoice"> 593 <conditional name="formatChoice">
566 <param name="format_select" value="bigwig"/> 594 <param name="format_select" value="bigwig"/>
567 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> 595 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
596 <param name="longLabel" value="RNA-Seq Coverage" />
568 <param name="track_color" value="#000000"/> 597 <param name="track_color" value="#000000"/>
569 </conditional> 598 </conditional>
570 </repeat> 599 </repeat>
571 </repeat> 600 </repeat>
572 <output name="output" file="bigwig/bigwig.html"> 601 <output name="output" file="bigwig/bigwig.html">
573 <!-- Verify tracks folder contains bam and bai --> 602 <extra_files type="file"
574 <extra_files type="file" 603 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
575 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" 604 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
576 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" 605 compare="sim_size"
577 compare="sim_size" 606 />
578 /> 607 <expand macro="verify_hub_structure" test="bigwig" />
579 <!-- Verify trackDb.txt contains the basic fields for a bam --> 608 <!-- check additional trackDb settings for BigWig -->
580 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> 609 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
610 <assert_contents>
611 <has_text text="autoScale"/>
612 <has_text text="maxHeightPixels"/>
613 <has_text text="windowingFunction"/>
614 </assert_contents>
615 </extra_files>
581 </output> 616 </output>
582 </test> 617 </test>
583 618
584 <!-- Test with GFF3 --> 619 <!-- Test with GFF3 -->
585 <test> 620 <test>
589 <param name="group_name" value="Default group"/> 624 <param name="group_name" value="Default group"/>
590 <repeat name="format"> 625 <repeat name="format">
591 <conditional name="formatChoice"> 626 <conditional name="formatChoice">
592 <param name="format_select" value="gff3"/> 627 <param name="format_select" value="gff3"/>
593 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/> 628 <param name="GFF3" value="gff3/inputs/Augustus_Gene_Predictions"/>
629 <param name="longLabel" value="Augustus" />
594 <param name="track_color" value="#000000"/> 630 <param name="track_color" value="#000000"/>
595 </conditional> 631 </conditional>
596 </repeat> 632 </repeat>
597 </repeat> 633 </repeat>
598 <output name="output" file="gff3/gff3_trackhub.html"> 634 <output name="output" file="gff3/gff3_trackhub.html">
599 <!-- Verify tracks folder contains bam and bai -->
600 <extra_files type="file" 635 <extra_files type="file"
601 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" 636 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
602 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" 637 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
603 compare="sim_size" 638 compare="sim_size"
604 /> 639 />
605 <!-- Verify trackDb.txt contains the basic fields for a bam --> 640 <expand macro="verify_hub_structure" test="gff3" />
606 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
607 </output> 641 </output>
608 </test> 642 </test>
609 643
610 <!-- Test with GTF --> 644 <!-- Test with GTF -->
611 <test> 645 <test>
615 <param name="group_name" value="Default group"/> 649 <param name="group_name" value="Default group"/>
616 <repeat name="format"> 650 <repeat name="format">
617 <conditional name="formatChoice"> 651 <conditional name="formatChoice">
618 <param name="format_select" value="gtf"/> 652 <param name="format_select" value="gtf"/>
619 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> 653 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
654 <param name="longLabel" value="StringTie transcripts" />
620 <param name="track_color" value="#000000"/> 655 <param name="track_color" value="#000000"/>
621 </conditional> 656 </conditional>
622 </repeat> 657 </repeat>
623 </repeat> 658 </repeat>
624 <output name="output" file="gtf/gtf_trackhub.html"> 659 <output name="output" file="gtf/gtf_trackhub.html">
625 <!-- Verify tracks folder contains bam and bai -->
626 <extra_files type="file" 660 <extra_files type="file"
627 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" 661 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
628 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" 662 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
629 compare="sim_size" 663 compare="sim_size"
630 /> 664 />
631 <!-- Verify trackDb.txt contains the basic fields for a bam --> 665 <expand macro="verify_hub_structure" test="gtf" />
632 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> 666 </output>
667 </test>
668
669 <!-- Test with BLAT Alignment -->
670 <test>
671 <param name="genome_name" value="Dbia3"/>
672 <param name="fasta_file" value="common/dbia3.fa"/>
673 <repeat name="group">
674 <param name="group_name" value="Default group"/>
675 <repeat name="format">
676 <conditional name="formatChoice">
677 <param name="format_select" value="bed" />
678 <conditional name="bedChoice">
679 <param name="bed_select" value="bed_blat_alignment_option"/>
680 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
681 <param name="longLabel" value="BLAT alignment" />
682 <param name="track_color" value="#000000"/>
683 <param name="database" value="NCBI" />
684 </conditional>
685 </conditional>
686 </repeat>
687 </repeat>
688 <output name="output" file="bed_blat_alignment/blat_alignment_trackhub.html">
689 <extra_files type="file"
690 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
691 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
692 compare="sim_size"
693 />
694 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
695 <!-- check additional trackDb settings for BLAT -->
696 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
697 <assert_contents>
698 <has_text text="searchIndex"/>
699 <has_text text="url"/>
700 <has_text text="urlLabel"/>
701 <has_text text="iframeUrl"/>
702 <has_text text="iframeOptions"/>
703 </assert_contents>
704 </extra_files>
705 </output>
706 </test>
707
708 <!-- Test with BLAST Alignment -->
709 <test>
710 <param name="genome_name" value="Dbia3"/>
711 <param name="fasta_file" value="common/dbia3.fa"/>
712 <repeat name="group">
713 <param name="group_name" value="Default group"/>
714 <repeat name="format">
715 <conditional name="formatChoice">
716 <param name="format_select" value="bed" />
717 <conditional name="bedChoice">
718 <param name="bed_select" value="bed_blast_alignment_option"/>
719 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
720 <param name="longLabel" value="BLAST alignment" />
721 <param name="track_color" value="#000000"/>
722 <param name="database" value="NCBI" />
723 </conditional>
724 </conditional>
725 </repeat>
726 </repeat>
727 <output name="output" file="bed_blast_alignment/blast_alignment_trackhub.html">
728 <extra_files type="file"
729 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
730 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
731 compare="sim_size"
732 />
733 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
734 <!-- check additional trackDb settings for BLAST -->
735 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
736 <assert_contents>
737 <has_text text="searchIndex"/>
738 <has_text text="url"/>
739 <has_text text="urlLabel"/>
740 <has_text text="iframeUrl"/>
741 <has_text text="iframeOptions"/>
742 </assert_contents>
743 </extra_files>
744 </output>
745 </test>
746
747 <!-- Test with Regtools Splice Junctions -->
748 <test>
749 <param name="genome_name" value="Dbia3"/>
750 <param name="fasta_file" value="common/dbia3.fa"/>
751 <repeat name="group">
752 <param name="group_name" value="Default group"/>
753 <repeat name="format">
754 <conditional name="formatChoice">
755 <param name="format_select" value="bed" />
756 <conditional name="bedChoice">
757 <param name="bed_select" value="bed_splice_junctions_option"/>
758 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
759 <param name="longLabel" value="Splice junctions" />
760 <param name="track_color" value="#000000"/>
761 </conditional>
762 </conditional>
763 </repeat>
764 </repeat>
765 <output name="output" file="bed_splice_junctions/splice_junctions_trackhub.html">
766 <extra_files type="file"
767 name="myHub/Dbia3/tracks/regtools_junctions.bb"
768 value="bed_splice_junctions/myHub/Dbia3/tracks/regtools_junctions.bb"
769 compare="sim_size"
770 />
771 <expand macro="verify_hub_structure" test="bed_splice_junctions" />
772 </output>
773 </test>
774
775 <!-- Test with Cytoband -->
776 <test>
777 <param name="genome_name" value="Dbia3"/>
778 <param name="fasta_file" value="common/dbia3.fa"/>
779 <repeat name="group">
780 <param name="group_name" value="Default group"/>
781 <repeat name="format">
782 <conditional name="formatChoice">
783 <param name="format_select" value="bed" />
784 <conditional name="bedChoice">
785 <param name="bed_select" value="bed_cytoBand"/>
786 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
787 <param name="longLabel" value="Cytoband" />
788 <param name="track_color" value="#000000"/>
789 </conditional>
790 </conditional>
791 </repeat>
792 </repeat>
793 <output name="output" file="bed_cytoband/cytoband_trackhub.html">
794 <extra_files type="file"
795 name="myHub/Dbia3/tracks/Cytoband.bb"
796 value="bed_cytoband/myHub/Dbia3/tracks/Cytoband.bb"
797 compare="sim_size"
798 />
799 <expand macro="verify_hub_structure" test="bed_cytoband" />
800 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
801 <assert_contents>
802 <has_text text="track cytoBandIdeo"/>
803 </assert_contents>
804 </extra_files>
805 </output>
806 </test>
807
808 <!-- Test with bigBed -->
809 <test>
810 <param name="genome_name" value="Dbia3"/>
811 <param name="fasta_file" value="common/dbia3.fa"/>
812 <repeat name="group">
813 <param name="group_name" value="Default group"/>
814 <repeat name="format">
815 <conditional name="formatChoice">
816 <param name="format_select" value="bigbed"/>
817 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
818 <param name="longLabel" value="bigBed" />
819 <param name="track_color" value="#000000"/>
820 </conditional>
821 </repeat>
822 </repeat>
823 <output name="output" file="big_bed/bigbed_trackhub.html">
824 <extra_files type="file"
825 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
826 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
827 compare="sim_size"
828 />
829 <expand macro="verify_hub_structure" test="big_bed" />
633 </output> 830 </output>
634 </test> 831 </test>
635 832
636 <!-- Test with one group and multiple tracks --> 833 <!-- Test with one group and multiple tracks -->
637 <test> 834 <test>
653 <param name="track_color" value="#000000"/> 850 <param name="track_color" value="#000000"/>
654 </conditional> 851 </conditional>
655 </repeat> 852 </repeat>
656 </repeat> 853 </repeat>
657 <output name="output" file="gtf_gff/gtf_gff_trackhub.html"> 854 <output name="output" file="gtf_gff/gtf_gff_trackhub.html">
658 <!-- verify tracks folder contains bam and bai -->
659 <extra_files type="file" 855 <extra_files type="file"
660 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" 856 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
661 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" 857 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
662 compare="sim_size" 858 compare="sim_size"
663 /> 859 />
664 <extra_files type="file" 860 <extra_files type="file"
665 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" 861 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
666 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" 862 value="gff3/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
667 compare="sim_size" 863 compare="sim_size"
668 /> 864 />
669 <!-- verify trackdb.txt contains the basic fields for a bam --> 865 <expand macro="verify_hub_structure" test="gtf_gff" />
670 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition --> 866 </output>
671 </output> 867 </test>
672 </test> 868
673 869 <!-- Test with one group and all the supported datatypes -->
674 <!-- Test with one group and all the supported datatypes on 10/04/2016 -->
675 <test> 870 <test>
676 <param name="genome_name" value="Dbia3"/> 871 <param name="genome_name" value="Dbia3"/>
677 <param name="fasta_file" value="common/dbia3.fa"/> 872 <param name="fasta_file" value="common/dbia3.fa"/>
678 <repeat name="group"> 873 <repeat name="group">
679 <param name="group_name" value="Default group"/> 874 <param name="group_name" value="Default group"/>
713 </conditional> 908 </conditional>
714 </repeat> 909 </repeat>
715 <repeat name="format"> 910 <repeat name="format">
716 <conditional name="formatChoice"> 911 <conditional name="formatChoice">
717 <param name="format_select" value="bigwig"/> 912 <param name="format_select" value="bigwig"/>
718 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> 913 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
719 <param name="track_color" value="#000000"/> 914 <param name="track_color" value="#000000"/>
720 </conditional> 915 </conditional>
721 </repeat> 916 </repeat>
722 <repeat name="format"> 917 <repeat name="format">
723 <conditional name="formatChoice"> 918 <conditional name="formatChoice">
731 <param name="format_select" value="gtf"/> 926 <param name="format_select" value="gtf"/>
732 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/> 927 <param name="GTF" value="gtf/inputs/StringTie_Assembled_Transcripts"/>
733 <param name="track_color" value="#000000"/> 928 <param name="track_color" value="#000000"/>
734 </conditional> 929 </conditional>
735 </repeat> 930 </repeat>
931 <repeat name="format">
932 <conditional name="formatChoice">
933 <param name="format_select" value="bed" />
934 <conditional name="bedChoice">
935 <param name="bed_select" value="bed_cytoBand"/>
936 <param name="BED_cytoBand" ftype="bed" value="bed_cytoband/inputs/Cytoband"/>
937 <param name="track_color" value="#000000"/>
938 </conditional>
939 </conditional>
940 </repeat>
941 <repeat name="format">
942 <conditional name="formatChoice">
943 <param name="format_select" value="bed" />
944 <conditional name="bedChoice">
945 <param name="bed_select" value="bed_splice_junctions_option"/>
946 <param name="BED_splice_junctions" ftype="bed" value="bed_splice_junctions/inputs/regtools_junctions"/>
947 <param name="track_color" value="#000000"/>
948 </conditional>
949 </conditional>
950 </repeat>
951 <repeat name="format">
952 <conditional name="formatChoice">
953 <param name="format_select" value="bed" />
954 <conditional name="bedChoice">
955 <param name="bed_select" value="bed_blast_alignment_option"/>
956 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
957 <param name="track_color" value="#000000"/>
958 <param name="database" value="NCBI" />
959 </conditional>
960 </conditional>
961 </repeat>
962 <repeat name="format">
963 <conditional name="formatChoice">
964 <param name="format_select" value="bed" />
965 <conditional name="bedChoice">
966 <param name="bed_select" value="bed_blat_alignment_option"/>
967 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
968 <param name="track_color" value="#000000"/>
969 <param name="database" value="NCBI" />
970 </conditional>
971 </conditional>
972 </repeat>
736 </repeat> 973 </repeat>
737 <output name="output" file="all_datatypes/all_datatypes_trackhub.html"> 974 <output name="output" file="all_datatypes/all_datatypes_trackhub.html">
738 <!-- verify tracks folder contains all the files --> 975 <!-- verify tracks folder contains all the files -->
739 <extra_files type="file" 976 <extra_files type="file"
740 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" 977 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
760 name="myHub/Dbia3/tracks/blastXmlToPsl.bb" 997 name="myHub/Dbia3/tracks/blastXmlToPsl.bb"
761 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb" 998 value="all_datatypes/myHub/Dbia3/tracks/blastXmlToPsl.bb"
762 compare="sim_size" 999 compare="sim_size"
763 /> 1000 />
764 <extra_files type="file" 1001 <extra_files type="file"
765 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" 1002 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
766 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" 1003 value="all_datatypes/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
767 compare="sim_size" 1004 compare="sim_size"
768 /> 1005 />
769 <extra_files type="file" 1006 <extra_files type="file"
770 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" 1007 name="myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
771 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb" 1008 value="all_datatypes/myHub/Dbia3/tracks/Augustus_Gene_Predictions.bb"
774 <extra_files type="file" 1011 <extra_files type="file"
775 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" 1012 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
776 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" 1013 value="all_datatypes/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
777 compare="sim_size" 1014 compare="sim_size"
778 /> 1015 />
779 <!-- verify trackdb.txt contains the basic fields for a bam --> 1016 <extra_files type="file"
780 <!-- todo: find a way to check also that the whole common structure is intact too, without too much repetition --> 1017 name="myHub/Dbia3/tracks/Cytoband.bb"
781 </output> 1018 value="all_datatypes/myHub/Dbia3/tracks/Cytoband.bb"
782 </test> 1019 compare="sim_size"
783 1020 />
784 <!-- Test with two groups and no tracks --> 1021 <extra_files type="file"
1022 name="myHub/Dbia3/tracks/regtools_junctions.bb"
1023 value="all_datatypes/myHub/Dbia3/tracks/regtools_junctions.bb"
1024 compare="sim_size"
1025 />
1026 <extra_files type="file"
1027 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
1028 value="all_datatypes/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
1029 compare="sim_size"
1030 />
1031 <extra_files type="file"
1032 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
1033 value="all_datatypes/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
1034 compare="sim_size"
1035 />
1036 <expand macro="verify_hub_structure" test="all_datatypes" />
1037 </output>
1038 </test>
1039
1040 <!-- Test with two groups and no tracks -->
785 <test> 1041 <test>
786 <param name="genome_name" value="Dbia3"/> 1042 <param name="genome_name" value="Dbia3"/>
787 <param name="fasta_file" value="common/dbia3.fa"/> 1043 <param name="fasta_file" value="common/dbia3.fa"/>
788 <repeat name="group"> 1044 <repeat name="group">
789 <param name="group_name" value="Default group"/> 1045 <param name="group_name" value="Default group"/>
790 </repeat> 1046 </repeat>
791 <repeat name="group"> 1047 <repeat name="group">
792 <param name="group_name" value="Other group"/> 1048 <param name="group_name" value="Other group"/>
793 </repeat> 1049 </repeat>
794 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html"> 1050 <output name="output" file="two_groups_no_track/two_groups_no_track_trackhub.html">
795 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_no_track/myHub/genomes.txt"/> 1051 <expand macro="verify_hub_structure_no_track" test="two_groups_no_track" />
796 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_no_track/myHub/Dbia3.html"/>
797 <!-- Email could be different, but we need to ensure we still have the email line -->
798 <extra_files type="file" name="myHub/hub.txt" value="two_groups_no_track/myHub/hub.txt" lines_diff="2">
799 <assert_contents>
800 <has_text text="email"/>
801 </assert_contents>
802 </extra_files>
803 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
804 </extra_files>
805 <extra_files type="file" name="myHub/Dbia3/description.html"
806 value="two_groups_no_track/myHub/Dbia3/description.html"/>
807 </output> 1052 </output>
808 </test> 1053 </test>
809 1054
810 <!-- Test with two groups and one track in first --> 1055 <!-- Test with two groups and one track in first -->
811 <test> 1056 <test>
814 <repeat name="group"> 1059 <repeat name="group">
815 <param name="group_name" value="Default group"/> 1060 <param name="group_name" value="Default group"/>
816 <repeat name="format"> 1061 <repeat name="format">
817 <conditional name="formatChoice"> 1062 <conditional name="formatChoice">
818 <param name="format_select" value="bigwig"/> 1063 <param name="format_select" value="bigwig"/>
819 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> 1064 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
820 <param name="track_color" value="#000000"/> 1065 <param name="track_color" value="#000000"/>
821 </conditional> 1066 </conditional>
822 </repeat> 1067 </repeat>
823 </repeat> 1068 </repeat>
824 <repeat name="group"> 1069 <repeat name="group">
825 <param name="group_name" value="Other group"/> 1070 <param name="group_name" value="Other group"/>
826 </repeat> 1071 </repeat>
827 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html"> 1072 <output name="output" file="two_groups_one_track_first/two_groups_one_track_first_trackhub.html">
828 <!-- Check myHub structure -->
829 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_first/myHub/genomes.txt"/>
830 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_first/myHub/Dbia3.html"/>
831 <!-- Email could be different, but we need to ensure we still have the email line -->
832 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_first/myHub/hub.txt" lines_diff="2">
833 <assert_contents>
834 <has_text text="email"/>
835 </assert_contents>
836 </extra_files>
837 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
838 </extra_files>
839 <extra_files type="file" name="myHub/Dbia3/description.html"
840 value="two_groups_one_track_first/myHub/Dbia3/description.html"/>
841
842 <!-- Check tracks exist --> 1073 <!-- Check tracks exist -->
843 <extra_files type="file" 1074 <extra_files type="file"
844 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" 1075 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
845 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" 1076 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
846 compare="sim_size" 1077 compare="sim_size"
847 /> 1078 />
848 1079 <expand macro="verify_hub_structure" test="two_groups_one_track_first" />
849 <!-- Check the groups.txt exists and is properly populated -->
850 </output> 1080 </output>
851 </test> 1081 </test>
852 1082
853 <!-- Test with two groups and one track in both --> 1083 <!-- Test with two groups and one track in both -->
854 <test> 1084 <test>
857 <repeat name="group"> 1087 <repeat name="group">
858 <param name="group_name" value="Default group"/> 1088 <param name="group_name" value="Default group"/>
859 <repeat name="format"> 1089 <repeat name="format">
860 <conditional name="formatChoice"> 1090 <conditional name="formatChoice">
861 <param name="format_select" value="bigwig"/> 1091 <param name="format_select" value="bigwig"/>
862 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> 1092 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
863 <param name="track_color" value="#000000"/> 1093 <param name="track_color" value="#000000"/>
864 </conditional> 1094 </conditional>
865 </repeat> 1095 </repeat>
866 </repeat> 1096 </repeat>
867 <repeat name="group"> 1097 <repeat name="group">
873 <param name="track_color" value="#000000"/> 1103 <param name="track_color" value="#000000"/>
874 </conditional> 1104 </conditional>
875 </repeat> 1105 </repeat>
876 </repeat> 1106 </repeat>
877 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html"> 1107 <output name="output" file="two_groups_one_track_both/two_groups_one_track_both_trackhub.html">
878 <!-- Check myHub structure -->
879 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_one_track_both/myHub/genomes.txt"/>
880 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_one_track_both/myHub/Dbia3.html"/>
881 <!-- Email could be different, but we need to ensure we still have the email line -->
882 <extra_files type="file" name="myHub/hub.txt" value="two_groups_one_track_both/myHub/hub.txt"
883 lines_diff="2">
884 <assert_contents>
885 <has_text text="email"/>
886 </assert_contents>
887 </extra_files>
888 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
889 </extra_files>
890 <extra_files type="file" name="myHub/Dbia3/description.html"
891 value="two_groups_one_track_both/myHub/Dbia3/description.html"/>
892
893 <!-- Check tracks exist --> 1108 <!-- Check tracks exist -->
894 <!-- First group --> 1109 <!-- First group -->
895 <extra_files type="file" 1110 <extra_files type="file"
896 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" 1111 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
897 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" 1112 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
898 compare="sim_size" 1113 compare="sim_size"
899 /> 1114 />
900 1115
901 <!-- Second group --> 1116 <!-- Second group -->
902 <extra_files type="file" 1117 <extra_files type="file"
903 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" 1118 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
904 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" 1119 value="gtf/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
905 compare="sim_size" 1120 compare="sim_size"
906 /> 1121 />
1122 <expand macro="verify_hub_structure" test="two_groups_one_track_both" />
907 <!-- Check the groups.txt exists and is properly populated --> 1123 <!-- Check the groups.txt exists and is properly populated -->
908 </output> 1124 </output>
909 </test> 1125 </test>
910 1126
911 <!-- Test with two groups and multiple tracks in both --> 1127 <!-- Test with two groups and multiple tracks in both -->
915 <repeat name="group"> 1131 <repeat name="group">
916 <param name="group_name" value="Default group"/> 1132 <param name="group_name" value="Default group"/>
917 <repeat name="format"> 1133 <repeat name="format">
918 <conditional name="formatChoice"> 1134 <conditional name="formatChoice">
919 <param name="format_select" value="bigwig"/> 1135 <param name="format_select" value="bigwig"/>
920 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Summary"/> 1136 <param name="BIGWIG" value="bigwig/inputs/RNA-Seq_Alignment_Coverage"/>
921 <param name="track_color" value="#000000"/> 1137 <param name="track_color" value="#000000"/>
922 </conditional> 1138 </conditional>
923 </repeat> 1139 </repeat>
924 <repeat name="format"> 1140 <repeat name="format">
925 <conditional name="formatChoice"> 1141 <conditional name="formatChoice">
945 <param name="track_color" value="#000000"/> 1161 <param name="track_color" value="#000000"/>
946 </conditional> 1162 </conditional>
947 </repeat> 1163 </repeat>
948 </repeat> 1164 </repeat>
949 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html"> 1165 <output name="output" file="two_groups_multiple_tracks/two_groups_multiple_tracks_trackhub.html">
950 <!-- Check myHub structure -->
951 <extra_files type="file" name="myHub/genomes.txt" value="two_groups_multiple_tracks/myHub/genomes.txt"/>
952 <extra_files type="file" name="myHub/Dbia3.html" value="two_groups_multiple_tracks/myHub/Dbia3.html"/>
953 <!-- Email could be different, but we need to ensure we still have the email line -->
954 <extra_files type="file" name="myHub/hub.txt" value="two_groups_multiple_tracks/myHub/hub.txt"
955 lines_diff="2">
956 <assert_contents>
957 <has_text text="email"/>
958 </assert_contents>
959 </extra_files>
960 <extra_files type="file" name="myHub/Dbia3/Dbia3.2bit" value="common/Dbia3.2bit">
961 </extra_files>
962 <extra_files type="file" name="myHub/Dbia3/description.html"
963 value="two_groups_multiple_tracks/myHub/Dbia3/description.html"/>
964
965 <!-- Check tracks exist --> 1166 <!-- Check tracks exist -->
966 <!-- First group --> 1167 <!-- First group -->
967 <extra_files type="file" 1168 <extra_files type="file"
968 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" 1169 name="myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
969 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Summary.bigwig" 1170 value="bigwig/myHub/Dbia3/tracks/RNA-Seq_Alignment_Coverage.bigwig"
970 compare="sim_size" 1171 compare="sim_size"
971 /> 1172 />
972 <extra_files type="file" 1173 <extra_files type="file"
973 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" 1174 name="myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
974 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam" 1175 value="bam/myHub/Dbia3/tracks/HISAT2_Accepted_Hits.bam"
989 <extra_files type="file" 1190 <extra_files type="file"
990 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb" 1191 name="myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
991 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb" 1192 value="gff3_multi_fasta/myHub/Dbia3/tracks/Multi-Fasta_GlimmerHMM_Gene_Predictions.bb"
992 compare="sim_size" 1193 compare="sim_size"
993 /> 1194 />
994 <!-- Check the groups.txt exists and is properly populated --> 1195 <expand macro="verify_hub_structure" test="two_groups_multiple_tracks" />
995 </output> 1196 </output>
996 </test> 1197 </test>
997 1198
998 <!-- Test default color in a track --> 1199 <!-- Test default color in a track -->
999 <test> 1200 <test>
1008 <param name="track_color" value="#000000"/> 1209 <param name="track_color" value="#000000"/>
1009 </conditional> 1210 </conditional>
1010 </repeat> 1211 </repeat>
1011 </repeat> 1212 </repeat>
1012 <output name="output" file="default_color/default_color_trackhub.html"> 1213 <output name="output" file="default_color/default_color_trackhub.html">
1214 <expand macro="verify_hub_structure" test="default_color" />
1013 <!-- Verify trackDb.txt contains the color 0,0,0 --> 1215 <!-- Verify trackDb.txt contains the color 0,0,0 -->
1014 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="default_color/myHub/Dbia3/trackDb.txt"> 1216 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
1015 <assert_contents> 1217 <assert_contents>
1016 <has_text text="color 0,0,0"/> 1218 <has_text text="color 0,0,0"/>
1017 </assert_contents> 1219 </assert_contents>
1018 </extra_files> 1220 </extra_files>
1019 1221
1034 <param name="track_color" value="#8064a2"/> 1236 <param name="track_color" value="#8064a2"/>
1035 </conditional> 1237 </conditional>
1036 </repeat> 1238 </repeat>
1037 </repeat> 1239 </repeat>
1038 <output name="output" file="changed_color/changed_color_trackhub.html"> 1240 <output name="output" file="changed_color/changed_color_trackhub.html">
1241 <expand macro="verify_hub_structure" test="changed_color" />
1039 <!-- Verify trackDb.txt contains the color 128,100,162 --> 1242 <!-- Verify trackDb.txt contains the color 128,100,162 -->
1040 <extra_files type="file" name="myHub/Dbia3/trackDb.txt" value="changed_color/myHub/Dbia3/trackDb.txt"> 1243 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
1041 <assert_contents> 1244 <assert_contents>
1042 <has_text text="color 128,100,162"/> 1245 <has_text text="color 128,100,162"/>
1043 </assert_contents> 1246 </assert_contents>
1044 </extra_files> 1247 </extra_files>
1045 1248
1065 <extra_files type="file" 1268 <extra_files type="file"
1066 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" 1269 name="myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
1067 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb" 1270 value="stringtie_chromosome_end_coordinates/myHub/Dbia3/tracks/StringTie_Assembled_Transcripts.bb"
1068 compare="sim_size" 1271 compare="sim_size"
1069 /> 1272 />
1273 <expand macro="verify_hub_structure" test="stringtie_chromosome_end_coordinates" />
1070 1274
1071 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition --> 1275 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
1072 </output> 1276 </output>
1073 </test> 1277 </test>
1074 1278
1075 <!-- Test for big files? --> 1279 <!-- Test default label in a track -->
1076 1280 <test>
1077 <!-- Find tests that should fail --> 1281 <param name="genome_name" value="Dbia3"/>
1078 1282 <param name="fasta_file" value="common/dbia3.fa"/>
1283 <repeat name="group">
1284 <param name="group_name" value="Default group"/>
1285 <repeat name="format">
1286 <conditional name="formatChoice">
1287 <param name="format_select" value="bam"/>
1288 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
1289 <param name="track_color" value="#000000"/>
1290 </conditional>
1291 </repeat>
1292 </repeat>
1293 <output name="output" file="default_color/default_color_trackhub.html">
1294 <expand macro="verify_hub_structure" test="default_color" />
1295 <!-- Verify trackDb.txt contains default label -->
1296 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
1297 <assert_contents>
1298 <has_text text="longLabel HISAT2 Accepted Hits.bam"/>
1299 </assert_contents>
1300 </extra_files>
1301
1302 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
1303 </output>
1304 </test>
1305
1306 <!-- Test customized label in a track -->
1307 <test>
1308 <param name="genome_name" value="Dbia3"/>
1309 <param name="fasta_file" value="common/dbia3.fa"/>
1310 <repeat name="group">
1311 <param name="group_name" value="Default group"/>
1312 <repeat name="format">
1313 <conditional name="formatChoice">
1314 <param name="format_select" value="bam"/>
1315 <param name="BAM" value="bam/inputs/HISAT2_Accepted_Hits.bam"/>
1316 <param name="longLabel" value="HISAT sequence alignment" />
1317 <param name="track_color" value="#000000"/>
1318 </conditional>
1319 </repeat>
1320 </repeat>
1321 <output name="output" file="changed_label/changed_label_trackhub.html">
1322 <expand macro="verify_hub_structure" test="changed_label" />
1323 <!-- Verify trackDb.txt contains the customized label -->
1324 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
1325 <assert_contents>
1326 <has_text text="longLabel HISAT sequence alignment"/>
1327 </assert_contents>
1328 </extra_files>
1329
1330 <!-- TODO: Find a way to check also that the whole common structure is intact too, without too much repetition -->
1331 </output>
1332 </test>
1333
1334 <!-- Test TrixIndex for Blat alignment track -->
1335 <test>
1336 <param name="genome_name" value="Dbia3"/>
1337 <param name="fasta_file" value="common/dbia3.fa"/>
1338 <repeat name="group">
1339 <param name="group_name" value="Default group"/>
1340 <repeat name="format">
1341 <conditional name="formatChoice">
1342 <param name="format_select" value="bed" />
1343 <conditional name="bedChoice">
1344 <param name="bed_select" value="bed_blat_alignment_option"/>
1345 <param name="BED_blat_alignment" ftype="bed" value="bed_blat_alignment/inputs/BLAT_alignment_bigpsl"/>
1346 <param name="longLabel" value="BLAT alignment" />
1347 <param name="track_color" value="#000000"/>
1348 <param name="database" value="NCBI" />
1349 <conditional name="add_trix_index">
1350 <param name="add_trix_index_selector" value="yes" />
1351 <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
1352 </conditional>
1353 </conditional>
1354 </conditional>
1355 </repeat>
1356 </repeat>
1357 <param name="debug_mode" value="true" />
1358 <output name="output" file="trix_index_files/blat_alignment_trackhub.html">
1359 <extra_files type="file"
1360 name="myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
1361 value="bed_blat_alignment/myHub/Dbia3/tracks/BLAT_alignment_bigpsl.bb"
1362 compare="sim_size"
1363 />
1364 <expand macro="verify_hub_structure" test="bed_blat_alignment" />
1365 <!-- check additional trackDb settings for BLAT -->
1366 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
1367 <assert_contents>
1368 <has_text text="searchIndex"/>
1369 <has_text text="searchTrix"/>
1370 <has_text text="url"/>
1371 <has_text text="urlLabel"/>
1372 <has_text text="iframeUrl"/>
1373 <has_text text="iframeOptions"/>
1374 </assert_contents>
1375 </extra_files>
1376 <!-- check Trix index directory -->
1377 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ix"
1378 value="trix_index_files/blat_out.ix" />
1379 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigpsl.bb.ixx"
1380 value="trix_index_files/blat_out.ixx" />
1381 </output>
1382 </test>
1383
1384 <!-- Test TrixIndex for BLAST Alignment -->
1385 <test>
1386 <param name="genome_name" value="Dbia3"/>
1387 <param name="fasta_file" value="common/dbia3.fa"/>
1388 <repeat name="group">
1389 <param name="group_name" value="Default group"/>
1390 <repeat name="format">
1391 <conditional name="formatChoice">
1392 <param name="format_select" value="bed" />
1393 <conditional name="bedChoice">
1394 <param name="bed_select" value="bed_blast_alignment_option"/>
1395 <param name="BED_blast_alignment" ftype="bed" value="bed_blast_alignment/inputs/BLAST_alignment_bigpsl"/>
1396 <param name="longLabel" value="BLAST alignment" />
1397 <param name="track_color" value="#000000"/>
1398 <param name="database" value="NCBI" />
1399 <conditional name="add_trix_index">
1400 <param name="add_trix_index_selector" value="yes" />
1401 <param name="trix_index" value="trix_index_files/blast_out.ix,trix_index_files/blast_out.ixx" />
1402 </conditional>
1403 </conditional>
1404 </conditional>
1405 </repeat>
1406 </repeat>
1407 <param name="debug_mode" value="true" />
1408 <output name="output" file="trix_index_files/blast_alignment_trackhub.html">
1409 <extra_files type="file"
1410 name="myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
1411 value="bed_blast_alignment/myHub/Dbia3/tracks/BLAST_alignment_bigpsl.bb"
1412 compare="sim_size"
1413 />
1414 <expand macro="verify_hub_structure" test="bed_blast_alignment" />
1415 <!-- check additional trackDb settings for BLAST -->
1416 <extra_files type="file" name="myHub/Dbia3/trackDb.txt">
1417 <assert_contents>
1418 <has_text text="searchIndex"/>
1419 <has_text text="searchTrix"/>
1420 <has_text text="url"/>
1421 <has_text text="urlLabel"/>
1422 <has_text text="iframeUrl"/>
1423 <has_text text="iframeOptions"/>
1424 </assert_contents>
1425 </extra_files>
1426 <!-- check Trix index directory -->
1427 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ix"
1428 value="trix_index_files/blast_out.ix" />
1429 <extra_files type="file" name="myHub/Dbia3/trix/BLAST_alignment_bigpsl.bb.ixx"
1430 value="trix_index_files/blast_out.ixx" />
1431 </output>
1432 </test>
1433
1434 <!-- Test TrixIndex for BigBed -->
1435 <test>
1436 <param name="genome_name" value="Dbia3"/>
1437 <param name="fasta_file" value="common/dbia3.fa"/>
1438 <repeat name="group">
1439 <param name="group_name" value="Default group"/>
1440 <repeat name="format">
1441 <conditional name="formatChoice">
1442 <param name="format_select" value="bigbed"/>
1443 <param name="BIGBED" value="big_bed/inputs/BLAT_alignment_bigbed" />
1444 <param name="longLabel" value="bigBed" />
1445 <param name="track_color" value="#000000"/>
1446 <conditional name="add_trix_index">
1447 <param name="add_trix_index_selector" value="yes" />
1448 <param name="trix_index" value="trix_index_files/blat_out.ix,trix_index_files/blat_out.ixx" />
1449 <param name="trix_id" value="name" />
1450 </conditional>
1451 </conditional>
1452 </repeat>
1453 </repeat>
1454 <param name="debug_mode" value="true" />
1455 <output name="output" file="trix_index_files/bigbed_trackhub.html">
1456 <extra_files type="file"
1457 name="myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
1458 value="big_bed/myHub/Dbia3/tracks/BLAT_alignment_bigbed.bigbed"
1459 compare="sim_size"
1460 />
1461 <expand macro="verify_hub_structure" test="big_bed">
1462 <has_text text="searchIndex"/>
1463 <has_text text="searchTrix"/>
1464 </expand>
1465
1466 <!-- check Trix index directory -->
1467 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ix"
1468 value="trix_index_files/blat_out.ix" />
1469 <extra_files type="file" name="myHub/Dbia3/trix/BLAT_alignment_bigbed.bigbed.ixx"
1470 value="trix_index_files/blat_out.ixx" />
1471 </output>
1472 </test>
1473
1079 </tests> 1474 </tests>
1080 1475
1081 <help> 1476 <help>
1082 This Galaxy tool permits to prepare your files to be ready for 1477 This Galaxy tool permits to prepare your files to be ready for
1083 Assembly Hub visualization. 1478 Assembly Hub visualization.