Mercurial > repos > iuc > delly_lr
comparison lr.xml @ 0:629a0066003d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
author | iuc |
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date | Mon, 28 Sep 2020 07:45:41 +0000 |
parents | |
children | d5124d5c8131 |
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-1:000000000000 | 0:629a0066003d |
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1 <?xml version="1.0"?> | |
2 <tool id="delly_lr" name="Delly long-read (lr)" version="@TOOL_VERSION@+galaxy0" profile="18.01"> | |
3 <description>optimized calling and genotyping of 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 #for $i, $current in enumerate($samples) | |
12 ln -s '${current}' 'sample_${i}.bam' && | |
13 ln -s '${current.metadata.bam_index}' 'sample_${i}.bam.bai' && | |
14 #end for | |
15 | |
16 ## run | |
17 delly lr | |
18 ## generic options | |
19 --svtype $generic.svtype | |
20 --technology $generic.technology | |
21 --genome '$generic.genome' | |
22 #if $generic.exclude | |
23 --exclude '$generic.exclude' | |
24 #end if | |
25 --outfile 'result.bcf' | |
26 ## discovery options | |
27 --mapqual $discovery.mapqual | |
28 --minclip $discovery.minclip | |
29 --minrefsep $discovery.minrefsep | |
30 --maxreadsep $discovery.maxreadsep | |
31 ## genotyping options | |
32 #if $genotyping.vcffile | |
33 --vcffile '$genotyping.vcffile' | |
34 #end if | |
35 --geno-qual $genotyping.genoqual | |
36 #if 'dump' in $oo.out | |
37 --dump 'dump.tsv.gz' | |
38 #end if | |
39 ## samples | |
40 #for $i, $current in enumerate($samples) | |
41 'sample_${i}.bam' | |
42 #end for | |
43 | |
44 ## postprocessing | |
45 #if 'log' in $oo.out | |
46 |& tee 'log.txt' | |
47 #end if | |
48 #if 'vcf' in $oo.out | |
49 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.' | |
50 #end if | |
51 #if 'dump' in $oo.out | |
52 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.' | |
53 #end if | |
54 ]]></command> | |
55 <inputs> | |
56 <expand macro="samples"/> | |
57 <section name="generic" title="Generic options" expanded="true"> | |
58 <expand macro="genome"/> | |
59 <expand macro="svtype"/> | |
60 <expand macro="exclude"/> | |
61 <param argument="--technology" type="select" label="Select sequencing technology"> | |
62 <option value="ont" selected="true">Oxford Nanopore (ont)</option> | |
63 <option value="pb">Pacbio (pb)</option> | |
64 </param> | |
65 </section> | |
66 <section name="discovery" title="Discovery options" expanded="true"> | |
67 <param argument="--mapqual" type="integer" value="1" label="Set minimum mapping quality"/> | |
68 <expand macro="minclip"/> | |
69 <expand macro="minrefsep"/> | |
70 <expand macro="maxreadsep"/> | |
71 </section> | |
72 <section name="genotyping" title="Genotyping options" expanded="true"> | |
73 <expand macro="vcffile"/> | |
74 <expand macro="genoqual"/> | |
75 </section> | |
76 <section name="oo" title="Output options"> | |
77 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> | |
78 <option value="bcf" selected="true">BCF</option> | |
79 <option value="vcf">VCF</option> | |
80 <option value="dump">SV-reads</option> | |
81 <option value="log">Log</option> | |
82 </param> | |
83 </section> | |
84 </inputs> | |
85 <outputs> | |
86 <expand macro="vcf"/> | |
87 <expand macro="bcf"/> | |
88 <expand macro="dump"/> | |
89 <expand macro="log"/> | |
90 </outputs> | |
91 <tests> | |
92 <!-- no test implemented for parameter vcffile --> | |
93 | |
94 <!-- #1 default, single --> | |
95 <test expect_num_outputs="2"> | |
96 <param name="samples" value="normal.bam"/> | |
97 <section name="generic"> | |
98 <param name="genome" value="genome.fasta"/> | |
99 </section> | |
100 <section name="oo"> | |
101 <param name="out" value="vcf,bcf"/> | |
102 </section> | |
103 <output name="out_vcf"> | |
104 <assert_contents> | |
105 <has_size value="3661" delta="10"/> | |
106 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | |
107 </assert_contents> | |
108 </output> | |
109 <output name="out_bcf"> | |
110 <assert_contents> | |
111 <has_size value="1184" delta="10"/> | |
112 </assert_contents> | |
113 </output> | |
114 </test> | |
115 <!-- #2 default, multi; test data to small, results are empty --> | |
116 <test expect_num_outputs="3"> | |
117 <param name="samples" value="normal.bam,tumor.bam"/> | |
118 <section name="generic"> | |
119 <param name="genome" value="genome.fasta"/> | |
120 </section> | |
121 <section name="oo"> | |
122 <param name="out" value="vcf,bcf,log"/> | |
123 </section> | |
124 <output name="out_vcf"> | |
125 <assert_contents> | |
126 <has_size value="3667" delta="10"/> | |
127 </assert_contents> | |
128 </output> | |
129 <output name="out_bcf"> | |
130 <assert_contents> | |
131 <has_size value="1189" delta="10"/> | |
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 --> | |
141 <test expect_num_outputs="4"> | |
142 <param name="samples" value="normal.bam"/> | |
143 <section name="generic"> | |
144 <param name="genome" value="genome.fasta"/> | |
145 <param name="exclude" value="exclude.tsv"/> | |
146 </section> | |
147 <section name="oo"> | |
148 <param name="out" value="vcf,bcf,dump,log"/> | |
149 </section> | |
150 <output name="out_vcf"> | |
151 <assert_contents> | |
152 <has_size value="3661" delta="10"/> | |
153 </assert_contents> | |
154 </output> | |
155 <output name="out_bcf"> | |
156 <assert_contents> | |
157 <has_size value="1186" delta="10"/> | |
158 </assert_contents> | |
159 </output> | |
160 <output name="out_dump"> | |
161 <assert_contents> | |
162 <has_n_lines n="0"/> | |
163 </assert_contents> | |
164 </output> | |
165 <output name="out_log"> | |
166 <assert_contents> | |
167 <has_text_matching expression=".+Done.+"/> | |
168 </assert_contents> | |
169 </output> | |
170 </test> | |
171 <!-- #4 --> | |
172 <test expect_num_outputs="4"> | |
173 <param name="samples" value="normal.bam"/> | |
174 <section name="generic"> | |
175 <param name="genome" value="genome.fasta"/> | |
176 <param name="svtype" value="DEL"/> | |
177 <param name="technology" value="pb"/> | |
178 </section> | |
179 <section name="discovery"> | |
180 <param name="mapqual" value="2"/> | |
181 <param name="qualtra" value="19"/> | |
182 <param name="madcutoff" value="8"/> | |
183 <param name="minclip" value="24"/> | |
184 <param name="minrefsep" value="24"/> | |
185 <param name="maxreadsep" value="39"/> | |
186 </section> | |
187 <section name="genotyping"> | |
188 <param name="genoqual" value="4"/> | |
189 </section> | |
190 <section name="oo"> | |
191 <param name="out" value="vcf,bcf,dump,log"/> | |
192 </section> | |
193 <output name="out_bcf"> | |
194 <assert_contents> | |
195 <has_size value="1182" delta="10"/> | |
196 </assert_contents> | |
197 </output> | |
198 <output name="out_vcf"> | |
199 <assert_contents> | |
200 <has_size value="3661" delta="10"/> | |
201 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | |
202 </assert_contents> | |
203 </output> | |
204 <output name="out_dump"> | |
205 <assert_contents> | |
206 <has_size value="0"/> | |
207 </assert_contents> | |
208 </output> | |
209 <output name="out_log"> | |
210 <assert_contents> | |
211 <has_text_matching expression=".+"/> | |
212 </assert_contents> | |
213 </output> | |
214 </test> | |
215 <!-- #5 --> | |
216 <test expect_num_outputs="1"> | |
217 <param name="samples" value="normal.bam"/> | |
218 <section name="generic"> | |
219 <param name="genome" value="genome.fasta"/> | |
220 <param name="svtype" value="INS"/> | |
221 </section> | |
222 <section name="oo"> | |
223 <param name="out" value="vcf"/> | |
224 </section> | |
225 <output name="out_vcf"> | |
226 <assert_contents> | |
227 <has_size value="3661" delta="10"/> | |
228 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | |
229 </assert_contents> | |
230 </output> | |
231 </test> | |
232 <!-- #6 --> | |
233 <test expect_num_outputs="1"> | |
234 <param name="samples" value="normal.bam"/> | |
235 <section name="generic"> | |
236 <param name="genome" value="genome.fasta"/> | |
237 <param name="svtype" value="DUP"/> | |
238 </section> | |
239 <section name="oo"> | |
240 <param name="out" value="bcf"/> | |
241 </section> | |
242 <output name="out_bcf"> | |
243 <assert_contents> | |
244 <has_size value="1182" delta="10"/> | |
245 </assert_contents> | |
246 </output> | |
247 </test> | |
248 <!-- #7 --> | |
249 <test expect_num_outputs="1"> | |
250 <param name="samples" value="normal.bam"/> | |
251 <section name="generic"> | |
252 <param name="genome" value="genome.fasta"/> | |
253 <param name="svtype" value="INV"/> | |
254 </section> | |
255 <section name="oo"> | |
256 <param name="out" value="dump"/> | |
257 </section> | |
258 <output name="out_dump"> | |
259 <assert_contents> | |
260 <has_size value="0"/> | |
261 </assert_contents> | |
262 </output> | |
263 </test> | |
264 <!-- #8 --> | |
265 <test expect_num_outputs="1"> | |
266 <param name="samples" value="normal.bam"/> | |
267 <section name="generic"> | |
268 <param name="genome" value="genome.fasta"/> | |
269 <param name="svtype" value="BND"/> | |
270 </section> | |
271 <section name="oo"> | |
272 <param name="out" value="log"/> | |
273 </section> | |
274 <output name="out_log"> | |
275 <assert_contents> | |
276 <has_text_matching expression=".+"/> | |
277 </assert_contents> | |
278 </output> | |
279 </test> | |
280 </tests> | |
281 <help><![CDATA[ | |
282 .. class:: infomark | |
283 | |
284 **What it does** | |
285 | |
286 @WID@ | |
287 | |
288 Delly *lr* uses the long-read SV discovery mode. | |
289 | |
290 **Input** | |
291 | |
292 Delly *lr* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. Additionally a VCF/BCF file for genotyping can be applied. | |
293 | |
294 **Output** | |
295 | |
296 The output is available in BCF and VCF format. Additionally a output file for SV-reads is provided. | |
297 | |
298 .. class:: infomark | |
299 | |
300 **References** | |
301 | |
302 @REFERENCES@ | |
303 ]]></help> | |
304 <expand macro="citations"/> | |
305 </tool> |