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comparison jbrowseArchiveCreator.xml @ 6:237707a6b74d draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a500f7ab2119cc5faaf80393bd87428389d06880-dirty
author yating-l
date Thu, 15 Feb 2018 17:05:05 -0500
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5:e762f4b9e4bd 6:237707a6b74d
1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.0.1">
2 <description>
3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <requirements>
9 <requirement type="package" version="1.2">samtools</requirement>
10 <requirement type="package" version="1.9">numpy</requirement>
11 <requirement type="package" version="1.68">biopython</requirement>
12 <requirement type="package" version="340">ucsc_hac</requirement>
13 <requirement type="package" version="1.12.4">jbrowse_tools</requirement>
14 </requirements>
15
16 <stdio>
17 </stdio>
18
19 <command detect_errors="exit_code"><![CDATA[
20 mkdir -p $output.extra_files_path;
21
22 ## Dump the tool parameters into a JSON file
23 python $json_file parameters.json;
24
25 python $__tool_directory__/jbrowseArchiveCreator.py --data_json parameters.json -o $output
26 ]]></command>
27 <configfiles>
28 <configfile name="json_file">
29 import json
30 import sys
31
32 file_path = sys.argv[1]
33 #set global data_parameter_dict = {}
34
35 ## Ask the user to enter the genome name
36 #silent $data_parameter_dict.update({"genome_name": str($genome_name)})
37
38 ## Function to retrieve the data of the inputs
39 #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
40 #set false_path = str($input_to_prepare)
41 #set $data_dict = {"false_path": $false_path}
42
43 #set name = str($input_to_prepare.name)
44 #silent $data_dict.update({"name": $name})
45 #silent $data_dict.update($extra_data_dict)
46 ## Add the ordering by taking the tool form indexes
47 #silent $data_dict.update({"order_index": $order_index})
48
49 #if $datatype in $data_parameter_dict
50 #silent $data_parameter_dict[$datatype].append($data_dict)
51 #else
52 #set array_inputs = []
53 #silent $array_inputs.append($data_dict)
54 #silent $data_parameter_dict.update({$datatype: $array_inputs})
55 #end if
56 #end def
57
58 ## Get the number of digits from tracks, to have a unique integer from group index and track index
59
60 #set temp_max_digit = 0
61
62 #for $g in $group
63 #if len($g.format) > $temp_max_digit
64 #silent temp_max_digit = len($g.format)
65 #end if
66 #end for
67
68 #set nb_digits_max_track = len(str($temp_max_digit))
69
70 ## END Get the number of digits
71
72 #for $i_g, $g in enumerate( $group )
73 #for $i, $f in enumerate( $g.format )
74 ## Create the order index using index_group+1 concatenated with index_track
75 #set index_group_final = str($i_g + 1)
76 #set index_track_final = str($index_group_final) + str($i).zfill($nb_digits_max_track)
77
78 ## For each format, we have a few mandatory fields we store in a dict
79 #set track_color = str($f.formatChoice.track_color)
80 #set group_name = str($g.group_name)
81 #set longLabel = str($f.formatChoice.longLabel)
82 #set extra_data_dict = {"track_color": $track_color,
83 "group_name": $group_name,
84 "long_label": $longLabel}
85 #if $f.formatChoice.format_select == "bam"
86 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
87
88 ## Add Bam format specific fields
89 #silent $extra_data_dict.update({"index": $bam_index})
90
91 #silent $prepare_json("Bam", $f.formatChoice.BAM, $index_track_final, $extra_data_dict)
92 #end if
93 #if $f.formatChoice.format_select == "bed"
94 #if $f.formatChoice.bedChoice.bed_select == "bed_generic"
95 #silent $prepare_json("Bed", $f.formatChoice.bedChoice.BED_generic, $index_track_final,
96 $extra_data_dict)
97 #end if
98 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
99 #silent $prepare_json("BedSimpleRepeats", $f.formatChoice.bedChoice.BED_simple_repeats, $index_track_final,
100 $extra_data_dict)
101 #end if
102 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
103 #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
104 $extra_data_dict)
105 #end if
106 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
107 ##set database = str($f.formatChoice.bedChoice.database)
108 ##silent $extra_data_dict.update({"database": $database})
109 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
110 $extra_data_dict)
111 #end if
112 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
113 ##set database = str($f.formatChoice.bedChoice.database)
114 ##silent $extra_data_dict.update({"database": $database})
115 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
116 $extra_data_dict)
117 #end if
118 #end if
119 #if $f.formatChoice.format_select == "blastxml"
120 #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final,
121 extra_data_dict)
122 #end if
123 #if $f.formatChoice.format_select == "bigwig"
124 #silent $prepare_json("BigWig", $f.formatChoice.BIGWIG, $index_track_final,
125 $extra_data_dict)
126 #end if
127 #if $f.formatChoice.format_select == 'gff3'
128 #silent $prepare_json("Gff3", $f.formatChoice.GFF3, $index_track_final,
129 $extra_data_dict)
130 #end if
131 #if $f.formatChoice.format_select == "gtf"
132 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
133 #silent $prepare_json("Gtf", $f.formatChoice.GTF, $index_track_final,
134 $extra_data_dict)
135 #end if
136 #end for
137 #end for
138
139 ## We combine the fasta file dataset name with his false path in a JSON object
140 #set fasta_json = {"false_path": str($fasta_file), "name": str($fasta_file.name)}
141 $data_parameter_dict.update({"fasta": $fasta_json})
142
143 ## Retrieve the user email
144 #silent $data_parameter_dict.update({"user_email": str($__user_email__)})
145
146 #silent $data_parameter_dict.update({"tool_directory": str($__tool_directory__)})
147
148 #silent $data_parameter_dict.update({"extra_files_path": str($output.extra_files_path)})
149
150 #silent $data_parameter_dict.update({"debug_mode": str($advanced_options.debug_mode)})
151
152 with open(file_path, 'w') as f:
153 json.dump($data_parameter_dict, f)
154 </configfile>
155 </configfiles>
156
157 <inputs>
158 <param
159 name="genome_name"
160 type="text"
161 size="30"
162 value="unknown"
163 label="JBrowse Hub Name"
164 />
165 <param
166 format="fasta"
167 name="fasta_file"
168 type="data"
169 label="Reference genome"
170 />
171 <repeat name="group" title="New group">
172 <param type="text" name="group_name" label="Group name" value="Default group"/>
173 <repeat name="format" title="New track">
174 <conditional name="formatChoice">
175 <param name="format_select" type="select" label="Format">
176 <option value="bam" selected="true">BAM</option>
177 <option value="bed">BED</option>
178 <option value="blastxml">BlastXML</option>
179 <option value="bigwig">BigWig</option>
180 <option value="gff3">GFF3</option>
181 <option value="gtf">GTF</option>
182 </param>
183
184 <when value="bam">
185 <param
186 format="bam"
187 name="BAM"
188 type="data"
189 label="BAM File"
190 />
191 <param name="longLabel" type="text" size="30" value = "Sequence Alignment" label="Track label" />
192 <param name="track_color" type="color" label="Track color" value="#000000">
193 <sanitizer>
194 <valid initial="string.letters,string.digits">
195 <add value="#"/>
196 </valid>
197 </sanitizer>
198 </param>
199 </when>
200 <when value="bed">
201 <conditional name="bedChoice">
202 <param name="bed_select" type="select" label="Bed Choice">
203 <option value="bed_generic">BED format</option>
204 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
205 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
206 <option value="bed_blast_alignment_option">Blast alignments (bed12+12 / bigPsl.as)</option>
207 <option value="bed_blat_alignment_option">BLAT alignments (bigPsl / bigPsl.as)</option>
208 </param>
209 <when value="bed_generic">
210 <param
211 format="bed"
212 name="BED_generic"
213 type="data"
214 label="Bed File"
215 />
216 </when>
217 <when value="bed_simple_repeats_option">
218 <param
219 format="bed"
220 name="BED_simple_repeats"
221 type="data"
222 label="Bed Simple Repeats (Bed4+12) File"
223 />
224 </when>
225 <when value="bed_splice_junctions_option">
226 <param
227 format="bed"
228 name="BED_splice_junctions"
229 type="data"
230 label="Bed Splice Junctions (Bed12+1) File"
231 />
232 </when>
233 <when value="bed_blast_alignment_option">
234 <param
235 format="bed"
236 name="BED_blast_alignment"
237 type="data"
238 label="Bed Blast Alignments (Bed12+12) File"
239 />
240 </when>
241 <when value="bed_blat_alignment_option">
242 <param
243 format="bed"
244 name="BED_blat_alignment"
245 type="data"
246 label="Bed BLAT Alignments (bigPsl) File"
247 />
248 </when>
249 </conditional>
250 <param name="longLabel" type="text" size="30" label="Track label" />
251 <param name="track_color" type="color" label="Track color" value="#000000">
252 <sanitizer>
253 <valid initial="string.letters,string.digits">
254 <add value="#"/>
255 </valid>
256 </sanitizer>
257 </param>
258 </when>
259 <when value="blastxml">
260 <param
261 format="blastxml"
262 name="BlastXML"
263 type="data"
264 label="Blast Alignments File"
265 />
266 <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" />
267 <param name="track_color" type="color" label="Track color" value="#000000">
268 <sanitizer>
269 <valid initial="string.letters,string.digits">
270 <add value="#"/>
271 </valid>
272 </sanitizer>
273 </param>
274 </when>
275 <when value="bigwig">
276 <param
277 format="bigwig"
278 name="BIGWIG"
279 type="data"
280 label="BIGWIG File"
281 />
282 <param name="longLabel" type="text" size="30" value="Sequence Coverage" label="Track label" />
283 <param name="track_color" type="color" label="Track color" value="#000000">
284 <sanitizer>
285 <valid initial="string.letters,string.digits">
286 <add value="#"/>
287 </valid>
288 </sanitizer>
289 </param>
290 </when>
291 <when value="gff3">
292 <param
293 format="gff3"
294 name="GFF3"
295 type="data"
296 label="GFF3 File"
297 />
298 <param name="longLabel" type="text" size="30" value="Gene Prediction" label="Track name" />
299 <param name="track_color" type="color" label="Track color" value="#000000">
300 <sanitizer>
301 <valid initial="string.letters,string.digits">
302 <add value="#"/>
303 </valid>
304 </sanitizer>
305 </param>
306 </when>
307 <when value="gtf">
308 <param
309 format="gtf"
310 name="GTF"
311 type="data"
312 label="GTF File"
313 />
314 <param name="longLabel" type="text" size="30" value="Assembled Transcripts" label="Track name" />
315 <param name="track_color" type="color" label="Track color" value="#000000">
316 <sanitizer>
317 <valid initial="string.letters,string.digits">
318 <add value="#"/>
319 </valid>
320 </sanitizer>
321 </param>
322 </when>
323 </conditional>
324 </repeat>
325 </repeat>
326 <conditional name="advanced_options">
327 <param name="advanced_options_selector" type="select" label="Advanced options">
328 <option value="off" selected="true">Hide advanced options</option>
329 <option value="on">Display advanced options</option>
330 </param>
331 <!-- TODO: Avoid redundancy here -->
332 <when value="on">
333 <param name="debug_mode" type="select" label="Activate debug mode">
334 <option value="false" selected="true">No</option>
335 <option value="true">Yes</option>
336 <help>
337 Use this option if you are a G-OnRamp developer
338 </help>
339 </param>
340 </when>
341 <when value="off">
342 <param name="debug_mode" type="hidden"
343 value="false">
344 </param>
345 </when>
346 </conditional>
347 </inputs>
348
349 <outputs>
350 <data format="jbrowsehub" name="output" label="${tool.name}" />
351 </outputs>
352 <tests>
353 <test>
354 <param name="genome_name" value="Dbia3"/>
355 <param name="fasta_file" value="common/dbia3.fa"/>
356 <output name="output" file="only_genome/only_genome.html">
357 <!-- Use macro to check the whole common structure without repeated code -->
358 <expand macro="verify_hub_structure_no_track" test="only_genome" />
359 </output>
360 </test>
361 </tests>
362 <help>
363 This Galaxy tool will create a jbrowse hub which including binary datasets and json datasets that can be used for
364 JBrowse visualization.
365 </help>
366 <citations>
367 </citations>
368 </tool>