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comparison annotate.xml @ 0:fb00426402b0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sansa commit b9066cb246cbae9a24020a79cf53d2dd4462b77d"
author iuc
date Mon, 25 Jan 2021 17:50:47 +0000
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-1:000000000000 0:fb00426402b0
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>