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comparison jbrowse_hub.xml @ 0:804a93e87cc8 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f22711ea7a464bdaf4d5aaea07f2eacf967aa66e-dirty
author yating-l
date Wed, 12 Apr 2017 17:41:55 -0400
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1 <tool id="jbrowse_hub" name="JBrowse Hub Creator" version="1.0">
2 <description>
3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse
4 </description>
5
6 <requirements>
7 <requirement type="package" version="1.2">samtools</requirement>
8 <requirement type="package" version="1.9">numpy</requirement>
9 <requirement type="package" version="1.68">biopython</requirement>
10 <requirement type="package" version="1.0">ucsc_tools_340</requirement>
11 <requirement type="package" version="1.12.1">jbrowse_tools</requirement>
12 </requirements>
13
14 <stdio>
15 </stdio>
16
17 <command detect_errors="exit_code"><![CDATA[
18 python $__tool_directory__/jbrowse_hub.py
19 --fasta '$reference'
20 --genome_name '$genome_name'
21
22 #set galaxy_url = str($GALAXY_URL)
23 #set $jbrowse_url = galaxy_url.replace("8080", "80")
24 --jbrowse_host '$jbrowse_url'
25
26 ## json metadata recording from Remi's hub-archive-creator.xml
27 #import json
28 #set global data_parameter_dict = {}
29
30 ## Function to retrieve the data of the inputs
31 #def prepare_json($input_to_prepare, $extra_data_dict={})
32 #set false_path = str($input_to_prepare)
33 #set name = $input_to_prepare.name
34
35 #set data_dict = {"name": $name}
36 #silent data_dict.update($extra_data_dict)
37
38 #silent $data_parameter_dict.update({$false_path: $data_dict})
39
40 #end def
41
42 #for $g in $group
43 #for $f in $g.format
44 #set track_label = str($f.formatChoice.label)
45 #set group_name = str($g.group_name)
46 #set extra_data_dict = {"label" : $track_label, "category" : $group_name}
47 #if $f.formatChoice.format_select == 'bed'
48 #set track_color = str($f.formatChoice.track_color)
49 #silent extra_data_dict.update({"color" : $track_color})
50 #if $f.formatChoice.bedChoice.bed_select == 'bed_generic_option'
51 --bed $f.formatChoice.bedChoice.BED_generic
52 #silent $prepare_json($f.formatChoice.bedChoice.BED_generic, extra_data_dict)
53 #elif $f.formatChoice.bedChoice.bed_select == 'bed_simple_repeats_option'
54 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
55 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict)
56 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
57 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
58 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict)
59 #end if
60 #end if
61 #if $f.formatChoice.format_select == 'bam'
62 --bam $f.formatChoice.BAM
63 #silent $prepare_json($f.formatChoice.BAM, extra_data_dict)
64 #end if
65 #if $f.formatChoice.format_select == 'gff3'
66 #set track_color = str($f.formatChoice.track_color)
67 #silent extra_data_dict.update({"color" : $track_color})
68 #if $f.formatChoice.gff3Choice.gff3_select == 'gff3_generic'
69 --gff3 $f.formatChoice.gff3Choice.GFF3_generic
70 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_generic, extra_data_dict)
71 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_transcript'
72 --gff3_transcript $f.formatChoice.gff3Choice.GFF3_transcript
73 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_transcript, extra_data_dict)
74 #elif $f.formatChoice.gff3Choice.gff3_select == 'gff3_mrna'
75 --gff3_mrna $f.formatChoice.gff3Choice.GFF3_mrna
76 #silent $prepare_json($f.formatChoice.gff3Choice.GFF3_mrna, extra_data_dict)
77 #end if
78 #end if
79 #if $f.formatChoice.format_select == 'blastxml'
80 --blastxml $f.formatChoice.BlastXML
81 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
82 #end if
83 #if $f.formatChoice.format_select == 'gtf'
84 --gtf $f.formatChoice.GTF
85 #set track_color = str($f.formatChoice.track_color)
86 #silent extra_data_dict.update({"color" : $track_color})
87 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict)
88 #end if
89 #if $f.formatChoice.format_select == 'bigwig'
90 --bigwig $f.formatChoice.BIGWIG
91 #set pos_color = str($f.formatChoice.pos_color)
92 #set neg_color = str($f.formatChoice.neg_color)
93 #silent $extra_data_dict.update({"style" : {"pos_color" : $pos_color, "neg_color" : $neg_color}})
94 #silent $prepare_json($f.formatChoice.BIGWIG, extra_data_dict)
95 #end if
96 #end for
97 #end for
98
99 #set all_data_json = json.dumps($data_parameter_dict)
100 -j '$all_data_json'
101 -e '$output.extra_files_path'
102 -o '$output'
103
104 ]]></command>
105
106 <inputs>
107 <param name="GALAXY_URL" type="baseurl" value="" />
108 <param name="reference" type="data" format="fasta" label="Reference Genome" />
109 <param name="genome_name" type="text" size="30" value="unknown" label="Genome name" />
110 <repeat name="group" title="New group">
111 <param type="text" name="group_name" label="Group name" value="Default group"/>
112 <repeat name="format" title="New track">
113 <conditional name="formatChoice">
114 <param name="format_select" type="select" label="Format">
115 <option value="bam" selected="true">BAM</option>
116 <option value="bed">BED</option>
117 <option value="blastxml">BLASTXML</option>
118 <option value="bigwig">BIGWIG</option>
119 <option value="gff3">GFF3</option>
120 <option value="gtf">GTF</option>
121 </param>
122
123 <when value="bam">
124 <param
125 format="bam"
126 name="BAM"
127 type="data"
128 label="BAM File"
129 />
130 <param name="label" type="text" size="30" value = "Sequence Alignment" label="Track name" />
131 </when>
132 <when value="bed">
133 <conditional name="bedChoice">
134 <param name="bed_select" type="select" label="Bed Choice">
135 <option value="bed_generic_option">BED format</option>
136 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
137 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
138 </param>
139 <when value="bed_generic_option">
140 <param
141 format="bed"
142 name="BED_generic"
143 type="data"
144 label="Bed File"
145 />
146 </when>
147 <when value="bed_simple_repeats_option">
148 <param
149 format="bed"
150 name="BED_simple_repeats"
151 type="data"
152 label="Bed Simple Repeats (Bed4+12) File"
153 />
154 </when>
155 <when value="bed_splice_junctions_option">
156 <param
157 format="bed"
158 name="BED_splice_junctions"
159 type="data"
160 label="Bed Splice Junctions (Bed12+1) File"
161 />
162 </when>
163 </conditional>
164 <param name="label" type="text" size="30" value="BED file" label="Track name" />
165 <param name="track_color" type="color" label="Track color" value="#daa520">
166 <sanitizer>
167 <valid initial="string.letters,string.digits">
168 <add value="#"/>
169 </valid>
170 </sanitizer>
171 </param>
172 </when>
173 <when value="blastxml">
174 <param
175 format="blastxml"
176 name="BlastXML"
177 type="data"
178 label="Blast Alignments File"
179 />
180 <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" />
181 </when>
182 <when value="bigwig">
183 <param
184 format="bigwig"
185 name="BIGWIG"
186 type="data"
187 label="BIGWIG File"
188 />
189 <param name="label" type="text" size="30" value="Sequence Coverage" label="Track name" />
190 <param name="pos_color" type="color" label="Positive Coverage Color" value="#FFA600">
191 <sanitizer>
192 <valid initial="string.letters,string.digits">
193 <add value="#"/>
194 </valid>
195 </sanitizer>
196 </param>
197 <param name="neg_color" type="color" label="Negative Coverage Color" value="#005EFF">
198 <sanitizer>
199 <valid initial="string.letters,string.digits">
200 <add value="#"/>
201 </valid>
202 </sanitizer>
203 </param>
204 </when>
205 <when value="gff3">
206 <conditional name="gff3Choice">
207 <param name="gff3_select" type="select" label="gff3 type">
208 <option value="gff3_generic">GFF3 format</option>
209 <option value="gff3_transcript">GFF3 format output from gene prediction tools (e.g. Augustus), structure: gene->transcription->CDS</option>
210 <option value="gff3_mrna">GFF3 format output from gene prediction tools (e.g. SNAP), structure: gene->mRNA->CDS</option>
211 </param>
212 <when value="gff3_generic">
213 <param
214 format="gff3"
215 name="GFF3_generic"
216 type="data"
217 label="GFF3 File"
218 />
219 </when>
220 <when value="gff3_transcript">
221 <param
222 format="gff3"
223 name="GFF3_transcript"
224 type="data"
225 label="GFF3 File from gene prediction"
226 />
227 </when>
228 <when value="gff3_mrna">
229 <param
230 format="gff3"
231 name="GFF3_mrna"
232 type="data"
233 label="GFF3 File from gene prediction"
234 />
235 </when>
236 </conditional>
237 <param name="label" type="text" size="30" value="Gene Prediction" label="Track name" />
238 <param name="track_color" type="color" label="Track color" value="#daa520">
239 <sanitizer>
240 <valid initial="string.letters,string.digits">
241 <add value="#"/>
242 </valid>
243 </sanitizer>
244 </param>
245 </when>
246 <when value="gtf">
247 <param
248 format="gtf"
249 name="GTF"
250 type="data"
251 label="GTF File"
252 />
253 <param name="label" type="text" size="30" value="Assembled Transcripts" label="Track name" />
254 <param name="track_color" type="color" label="Track color" value="#daa520">
255 <sanitizer>
256 <valid initial="string.letters,string.digits">
257 <add value="#"/>
258 </valid>
259 </sanitizer>
260 </param>
261 </when>
262 </conditional>
263 </repeat>
264 </repeat>
265 </inputs>
266
267 <outputs>
268 <data format="html" name="output" label="${tool.name}" />
269 </outputs>
270 <tests>
271 <test>
272 <param name="reference" value="dbia3/raw/dbia3.fa" />
273 <param name="output" value="hubtest" />
274 <repeat name="group">
275 <param name="group_name" value="Default group"/>
276 <repeat name="format">
277 <conditional name="formatChoice">
278 <param name="format_select" value="gff3_transcript"/>
279 <param name="GFF3_transcript" value="dbia3/raw/Augustus_on_data_3__GTF_GFF.gff3" />
280 </conditional>
281 </repeat>
282 </repeat>
283 <output name="output" file="hubtest" >
284 </output>
285 </test>
286 </tests>
287 <help>
288 This Galaxy tool will create a tar file which including raw datasets and json datasets that can be used for
289 JBrowse visualization.
290 </help>
291 <citations>
292 </citations>
293 </tool>