Mercurial > repos > iuc > sansa_annotate
comparison annotate.xml @ 0:fb00426402b0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
author | iuc |
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date | Mon, 25 Jan 2021 17:50:47 +0000 |
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children | e3862632706d |
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1 <?xml version="1.0"?> | |
2 <tool id="sansa_annotate" name="sansa annotate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01"> | |
3 <description>structural variants</description> | |
4 <macros> | |
5 <import>macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements"/> | |
8 <expand macro="version_command"/> | |
9 <command detect_errors="exit_code"><![CDATA[ | |
10 ## initialize | |
11 ## file format gtf.gz is required | |
12 #if $type_cond.type_sel == 'fg' or $type_cond.type_sel == 'sfg' | |
13 gzip -c '$type_cond.fg.gtf' > 'db.gtf.gz' && | |
14 #end if | |
15 | |
16 ## run | |
17 sansa annotate | |
18 ## sv annotation options | |
19 #if $type_cond.type_sel == 's' or $type_cond.type_sel == 'sfg' | |
20 --db '$type_cond.s.db' | |
21 --bpoffset $type_cond.s.bpoffset | |
22 --ratio $type_cond.s.ratio | |
23 --strategy '$type_cond.s.strategy' | |
24 $type_cond.s.notype | |
25 $type_cond.s.nomatch | |
26 #end if | |
27 ## feature and gene annotation options | |
28 #if $type_cond.type_sel == 'fg' or $type_cond.type_sel == 'sfg' | |
29 --gtf 'db.gtf.gz' | |
30 --id '$type_cond.fg.id' | |
31 --feature '$type_cond.fg.feature' | |
32 --distance $type_cond.fg.distance | |
33 #end if | |
34 ## input | |
35 '$input' | |
36 | |
37 ## postprocessing | |
38 2>&1 | tee -a '$out_log' | |
39 ]]></command> | |
40 <inputs> | |
41 <param name="input" type="data" format="vcf" label="Select input file"/> | |
42 <conditional name="type_cond"> | |
43 <param name="type_sel" type="select" label="Select annotation mode(s)"> | |
44 <option value="s" selected="true">SV</option> | |
45 <option value="fg">Feature/Gene</option> | |
46 <option value="sfg">SV and Feature/Gene</option> | |
47 </param> | |
48 <when value="s"> | |
49 <expand macro="s"/> | |
50 </when> | |
51 <when value="fg"> | |
52 <expand macro="fg"/> | |
53 </when> | |
54 <when value="sfg"> | |
55 <expand macro="s"/> | |
56 <expand macro="fg"/> | |
57 </when> | |
58 </conditional> | |
59 <section name="oo" title="Output options" expanded="true"> | |
60 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> | |
61 <option value="anno" selected="true">Annotation</option> | |
62 <option value="log">Log</option> | |
63 <option value="query">Query SV</option> | |
64 </param> | |
65 </section> | |
66 </inputs> | |
67 <outputs> | |
68 <data name="out_anno" format="bcf" from_work_dir="anno.bcf" label="${tool.name} on ${on_string}: Annotation"> | |
69 <filter>'anno' in oo['out']</filter> | |
70 </data> | |
71 <data name="out_query" format="tabular.gz" from_work_dir="query.tsv.gz" label="${tool.name} on ${on_string}: Query SV"> | |
72 <filter>'query' in oo['out']</filter> | |
73 </data> | |
74 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log"> | |
75 <filter>'log' in oo['out']</filter> | |
76 </data> | |
77 </outputs> | |
78 <tests> | |
79 <!-- #1 s, default --> | |
80 <test expect_num_outputs="3"> | |
81 <param name="input" value="input.vcf"/> | |
82 <conditional name="type_cond"> | |
83 <param name="type_sel" value="s"/> | |
84 <section name="s"> | |
85 <param name="db" value="db.vcf"/> | |
86 </section> | |
87 </conditional> | |
88 <section name="oo"> | |
89 <param name="out" value="anno,log,query"/> | |
90 </section> | |
91 <output name="out_anno"> | |
92 <assert_contents> | |
93 <has_size value="57072"/> | |
94 </assert_contents> | |
95 </output> | |
96 <output name="out_query"> | |
97 <assert_contents> | |
98 <has_size value="91"/> | |
99 </assert_contents> | |
100 </output> | |
101 <output name="out_log"> | |
102 <assert_contents> | |
103 <has_text_matching expression=".+Done.+"/> | |
104 </assert_contents> | |
105 </output> | |
106 </test> | |
107 <!-- #2 s, custom --> | |
108 <test expect_num_outputs="3"> | |
109 <param name="input" value="input.vcf"/> | |
110 <conditional name="type_cond"> | |
111 <param name="type_sel" value="s"/> | |
112 <section name="s"> | |
113 <param name="db" value="db.vcf"/> | |
114 <param name="bpoffset" value="51"/> | |
115 <param name="ratio" value="0.79"/> | |
116 <param name="strategy" value="all"/> | |
117 <param name="notype" value="true"/> | |
118 <param name="nomatch" value="true"/> | |
119 </section> | |
120 </conditional> | |
121 <section name="oo"> | |
122 <param name="out" value="anno,log,query"/> | |
123 </section> | |
124 <output name="out_anno"> | |
125 <assert_contents> | |
126 <has_size value="57072"/> | |
127 </assert_contents> | |
128 </output> | |
129 <output name="out_query"> | |
130 <assert_contents> | |
131 <has_size value="91"/> | |
132 </assert_contents> | |
133 </output> | |
134 <output name="out_log"> | |
135 <assert_contents> | |
136 <has_text_matching expression=".+Done.+"/> | |
137 </assert_contents> | |
138 </output> | |
139 </test> | |
140 <!-- #3 fg, default --> | |
141 <test expect_num_outputs="3"> | |
142 <param name="input" value="input.vcf"/> | |
143 <conditional name="type_cond"> | |
144 <param name="type_sel" value="fg"/> | |
145 <section name="fg"> | |
146 <param name="gtf" value="db.gtf"/> | |
147 </section> | |
148 </conditional> | |
149 <section name="oo"> | |
150 <param name="out" value="anno,log,query"/> | |
151 </section> | |
152 <output name="out_anno"> | |
153 <assert_contents> | |
154 <has_size value="2408"/> | |
155 </assert_contents> | |
156 </output> | |
157 <output name="out_query"> | |
158 <assert_contents> | |
159 <has_size value="91"/> | |
160 </assert_contents> | |
161 </output> | |
162 <output name="out_log"> | |
163 <assert_contents> | |
164 <has_text_matching expression=".+Done.+"/> | |
165 </assert_contents> | |
166 </output> | |
167 </test> | |
168 <!-- #4 fg, custom --> | |
169 <test expect_num_outputs="3"> | |
170 <param name="input" value="input.vcf"/> | |
171 <conditional name="type_cond"> | |
172 <param name="type_sel" value="fg"/> | |
173 <section name="fg"> | |
174 <param name="gtf" value="db.gtf"/> | |
175 <param name="id" value="gene_id"/> | |
176 <param name="feature" value="exon"/> | |
177 <param name="distance" value="1001"/> | |
178 </section> | |
179 </conditional> | |
180 <section name="oo"> | |
181 <param name="out" value="anno,log,query"/> | |
182 </section> | |
183 <output name="out_anno"> | |
184 <assert_contents> | |
185 <has_size value="2408"/> | |
186 </assert_contents> | |
187 </output> | |
188 <output name="out_query"> | |
189 <assert_contents> | |
190 <has_size value="91"/> | |
191 </assert_contents> | |
192 </output> | |
193 <output name="out_log"> | |
194 <assert_contents> | |
195 <has_text_matching expression=".+Done.+"/> | |
196 </assert_contents> | |
197 </output> | |
198 </test> | |
199 <!-- #5 sfg, default --> | |
200 <test expect_num_outputs="3"> | |
201 <param name="input" value="input.vcf"/> | |
202 <conditional name="type_cond"> | |
203 <param name="type_sel" value="sfg"/> | |
204 <section name="s"> | |
205 <param name="db" value="db.vcf"/> | |
206 </section> | |
207 <section name="fg"> | |
208 <param name="gtf" value="db.gtf"/> | |
209 </section> | |
210 </conditional> | |
211 <section name="oo"> | |
212 <param name="out" value="anno,log,query"/> | |
213 </section> | |
214 <output name="out_anno"> | |
215 <assert_contents> | |
216 <has_size value="57072"/> | |
217 </assert_contents> | |
218 </output> | |
219 <output name="out_query"> | |
220 <assert_contents> | |
221 <has_size value="91"/> | |
222 </assert_contents> | |
223 </output> | |
224 <output name="out_log"> | |
225 <assert_contents> | |
226 <has_text_matching expression=".+Done.+"/> | |
227 </assert_contents> | |
228 </output> | |
229 </test> | |
230 <!-- #5 sfg, custom --> | |
231 <test expect_num_outputs="3"> | |
232 <param name="input" value="input.vcf"/> | |
233 <conditional name="type_cond"> | |
234 <param name="type_sel" value="sfg"/> | |
235 <section name="s"> | |
236 <param name="db" value="db.vcf"/> | |
237 <param name="bpoffset" value="51"/> | |
238 <param name="ratio" value="0.79"/> | |
239 <param name="strategy" value="all"/> | |
240 <param name="notype" value="true"/> | |
241 <param name="nomatch" value="true"/> | |
242 </section> | |
243 <section name="fg"> | |
244 <param name="gtf" value="db.gtf"/> | |
245 <param name="id" value="gene_id"/> | |
246 <param name="feature" value="exon"/> | |
247 <param name="distance" value="1001"/> | |
248 </section> | |
249 </conditional> | |
250 <section name="oo"> | |
251 <param name="out" value="anno,log,query"/> | |
252 </section> | |
253 <output name="out_anno"> | |
254 <assert_contents> | |
255 <has_size value="57072"/> | |
256 </assert_contents> | |
257 </output> | |
258 <output name="out_query"> | |
259 <assert_contents> | |
260 <has_size value="91"/> | |
261 </assert_contents> | |
262 </output> | |
263 <output name="out_log"> | |
264 <assert_contents> | |
265 <has_text_matching expression=".+Done.+"/> | |
266 </assert_contents> | |
267 </output> | |
268 </test> | |
269 </tests> | |
270 <help><![CDATA[ | |
271 .. class:: infomark | |
272 | |
273 **What it does** | |
274 | |
275 Sansa *annotate* is a structural variant (SV) annotation tool. | |
276 | |
277 **Input** | |
278 | |
279 - sample (VCF) | |
280 - gene annotation file (GTF/GFF2/GFF3) | |
281 - annotation database, e.g. `gnomAD-SV <https://gnomad.broadinstitute.org/>`_ or `1000 Genomes phase 3 <https://www.internationalgenome.org/phase-3-structural-variant-dataset>`_ | |
282 | |
283 **Output** | |
284 | |
285 - anno (BCF) with annotation SVs augmented by a unique ID (INFO/ANNOID) | |
286 - query (tabular.gz) with query SVs matched to annotation IDs | |
287 | |
288 .. class:: infomark | |
289 | |
290 **References** | |
291 | |
292 More information are available on `GitHub <https://github.com/dellytools/sansa>`_. | |
293 ]]></help> | |
294 <citations> | |
295 <citation type="doi">10.1093/bioinformatics/bts378</citation> | |
296 </citations> | |
297 </tool> |