Mercurial > repos > iuc > delly_lr
comparison lr.xml @ 2:ceda4714f3a1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
author | iuc |
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date | Fri, 22 Jan 2021 14:32:45 +0000 |
parents | d5124d5c8131 |
children | d30785dbe6b7 |
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1:d5124d5c8131 | 2:ceda4714f3a1 |
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7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
9 <command detect_errors="exit_code"><![CDATA[ | 9 <command detect_errors="exit_code"><![CDATA[ |
10 ## initialize | 10 ## initialize |
11 @BAM@ | 11 @BAM@ |
12 | 12 |
13 ## run | 13 ## run |
14 delly lr | 14 delly lr |
15 ## generic options | 15 ## generic options |
16 --svtype $generic.svtype | 16 --svtype $generic.svtype |
17 --technology $generic.technology | 17 --technology $generic.technology |
24 --mapqual $discovery.mapqual | 24 --mapqual $discovery.mapqual |
25 --minclip $discovery.minclip | 25 --minclip $discovery.minclip |
26 --min-clique-size $discovery.mincliquesize | 26 --min-clique-size $discovery.mincliquesize |
27 --minrefsep $discovery.minrefsep | 27 --minrefsep $discovery.minrefsep |
28 --maxreadsep $discovery.maxreadsep | 28 --maxreadsep $discovery.maxreadsep |
29 ## consensus options | |
30 --max-reads $consensus.maxreads | |
31 --flank-size $consensus.flanksize | |
32 --flank-quality $consensus.flankquality | |
29 ## genotyping options | 33 ## genotyping options |
30 #if $genotyping.vcffile | |
31 --vcffile '$genotyping.vcffile' | |
32 #end if | |
33 --geno-qual $genotyping.genoqual | 34 --geno-qual $genotyping.genoqual |
34 #if 'dump' in $oo.out | 35 #if 'dump' in $oo.out |
35 --dump 'dump.tsv.gz' | 36 --dump 'dump.tsv.gz' |
36 #end if | 37 #end if |
37 ## samples | 38 ## input |
38 #for $i, $current in enumerate($samples) | 39 #for $i, $current in enumerate($input) |
39 'sample_${i}.bam' | 40 'input_${i}.bam' |
40 #end for | 41 #end for |
41 | 42 |
42 ## postprocessing | 43 ## postprocessing |
43 @LOG@ | 44 @LOG@ |
45 @DUMP@ | |
44 @VCF@ | 46 @VCF@ |
45 @DUMP@ | |
46 ]]></command> | 47 ]]></command> |
47 <inputs> | 48 <inputs> |
48 <expand macro="samples"/> | 49 <expand macro="input" format="bam" multiple="true" label="Select input file(s)"/> |
49 <section name="generic" title="Generic options" expanded="true"> | 50 <section name="generic" title="Generic options" expanded="true"> |
50 <expand macro="genome"/> | |
51 <expand macro="svtype"/> | 51 <expand macro="svtype"/> |
52 <expand macro="exclude"/> | |
53 <param argument="--technology" type="select" label="Select sequencing technology"> | 52 <param argument="--technology" type="select" label="Select sequencing technology"> |
54 <option value="ont" selected="true">Oxford Nanopore (ont)</option> | 53 <option value="ont" selected="true">Oxford Nanopore (ont)</option> |
55 <option value="pb">Pacbio (pb)</option> | 54 <option value="pb">PacBio (pb)</option> |
56 </param> | 55 </param> |
56 <expand macro="genome"/> | |
57 <expand macro="exclude"/> | |
57 </section> | 58 </section> |
58 <section name="discovery" title="Discovery options" expanded="true"> | 59 <section name="discovery" title="Discovery options" expanded="true"> |
59 <param argument="--mapqual" type="integer" value="1" label="Set minimum mapping quality"/> | 60 <param argument="--mapqual" type="integer" value="10" label="Set minimum mapping quality"/> |
60 <expand macro="minclip"/> | 61 <expand macro="minclip"/> |
61 <expand macro="mincliquesize"/> | 62 <expand macro="mincliquesize"/> |
62 <expand macro="minrefsep" defaut="30"/> | 63 <expand macro="minrefsep" default="30"/> |
63 <expand macro="maxreadsep" defaut="75"/> | 64 <expand macro="maxreadsep" default="75"/> |
65 </section> | |
66 <section name="consensus" title="Consensus options" expanded="true"> | |
67 <param name="maxreads" type="integer" value="5" label="Set maximum reads for consensus computation" help="(--max-reads)"/> | |
68 <param name="flanksize" type="integer" value="400" label="Set minimum flank size" help="(--flank-size)"/> | |
69 <param name="flankquality" type="float" min="0.0" max="1.0" value="0.9" label="Set minimum flank quality" help="(--flank-quality)"/> | |
64 </section> | 70 </section> |
65 <section name="genotyping" title="Genotyping options" expanded="true"> | 71 <section name="genotyping" title="Genotyping options" expanded="true"> |
66 <expand macro="vcffile"/> | |
67 <expand macro="genoqual"/> | 72 <expand macro="genoqual"/> |
68 </section> | 73 </section> |
69 <section name="oo" title="Output options"> | 74 <section name="oo" title="Output options" expanded="true"> |
70 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> | 75 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)"> |
71 <option value="bcf" selected="true">BCF</option> | 76 <option value="bcf" selected="true">BCF</option> |
77 <option value="log">Log</option> | |
78 <option value="dump">SV-reads</option> | |
72 <option value="vcf">VCF</option> | 79 <option value="vcf">VCF</option> |
73 <option value="dump">SV-reads</option> | |
74 <option value="log">Log</option> | |
75 </param> | 80 </param> |
76 </section> | 81 </section> |
77 </inputs> | 82 </inputs> |
78 <outputs> | 83 <outputs> |
79 <expand macro="vcf"/> | |
80 <expand macro="bcf"/> | 84 <expand macro="bcf"/> |
81 <expand macro="dump"/> | 85 <expand macro="dump"/> |
82 <expand macro="log"/> | 86 <expand macro="log"/> |
87 <expand macro="vcf"/> | |
83 </outputs> | 88 </outputs> |
84 <tests> | 89 <tests> |
85 <!-- no test implemented for parameter vcffile --> | |
86 | |
87 <!-- #1 default, single --> | 90 <!-- #1 default, single --> |
88 <test expect_num_outputs="2"> | 91 <test expect_num_outputs="2"> |
89 <param name="samples" value="normal.bam"/> | 92 <param name="input" value="normal.bam"/> |
90 <section name="generic"> | 93 <section name="generic"> |
91 <param name="genome" value="genome.fasta"/> | 94 <param name="genome" value="genome.fasta"/> |
92 </section> | 95 </section> |
93 <section name="oo"> | 96 <section name="oo"> |
94 <param name="out" value="vcf,bcf"/> | 97 <param name="out" value="vcf,bcf"/> |
95 </section> | 98 </section> |
99 <output name="out_bcf"> | |
100 <assert_contents> | |
101 <has_size value="1184" delta="10"/> | |
102 </assert_contents> | |
103 </output> | |
96 <output name="out_vcf"> | 104 <output name="out_vcf"> |
97 <assert_contents> | 105 <assert_contents> |
98 <has_size value="3661" delta="10"/> | 106 <has_size value="3661" delta="10"/> |
99 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | 107 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> |
100 </assert_contents> | 108 </assert_contents> |
101 </output> | 109 </output> |
102 <output name="out_bcf"> | |
103 <assert_contents> | |
104 <has_size value="1184" delta="10"/> | |
105 </assert_contents> | |
106 </output> | |
107 </test> | 110 </test> |
108 <!-- #2 default, multi; test data to small, results are empty --> | 111 <!-- #2 default, multi; test data to small, results are empty --> |
109 <test expect_num_outputs="3"> | 112 <test expect_num_outputs="3"> |
110 <param name="samples" value="normal.bam,tumor.bam"/> | 113 <param name="input" value="normal.bam,tumor.bam"/> |
111 <section name="generic"> | 114 <section name="generic"> |
112 <param name="genome" value="genome.fasta"/> | 115 <param name="genome" value="genome.fasta"/> |
113 </section> | 116 </section> |
114 <section name="oo"> | 117 <section name="oo"> |
115 <param name="out" value="vcf,bcf,log"/> | 118 <param name="out" value="vcf,bcf,log"/> |
116 </section> | 119 </section> |
120 <output name="out_bcf"> | |
121 <assert_contents> | |
122 <has_size value="1189" delta="10"/> | |
123 </assert_contents> | |
124 </output> | |
125 <output name="out_log"> | |
126 <assert_contents> | |
127 <has_text_matching expression=".+Done.+"/> | |
128 </assert_contents> | |
129 </output> | |
117 <output name="out_vcf"> | 130 <output name="out_vcf"> |
118 <assert_contents> | 131 <assert_contents> |
119 <has_size value="3667" delta="10"/> | 132 <has_size value="3667" delta="10"/> |
120 </assert_contents> | |
121 </output> | |
122 <output name="out_bcf"> | |
123 <assert_contents> | |
124 <has_size value="1189" delta="10"/> | |
125 </assert_contents> | |
126 </output> | |
127 <output name="out_log"> | |
128 <assert_contents> | |
129 <has_text_matching expression=".+Done.+"/> | |
130 </assert_contents> | 133 </assert_contents> |
131 </output> | 134 </output> |
132 </test> | 135 </test> |
133 <!-- #3 --> | 136 <!-- #3 --> |
134 <test expect_num_outputs="4"> | 137 <test expect_num_outputs="4"> |
135 <param name="samples" value="normal.bam"/> | 138 <param name="input" value="normal.bam"/> |
136 <section name="generic"> | 139 <section name="generic"> |
137 <param name="genome" value="genome.fasta"/> | 140 <param name="genome" value="genome.fasta"/> |
138 <param name="exclude" value="exclude.tsv"/> | 141 <param name="exclude" value="exclude.tsv"/> |
139 </section> | 142 </section> |
140 <section name="oo"> | 143 <section name="oo"> |
141 <param name="out" value="vcf,bcf,dump,log"/> | 144 <param name="out" value="vcf,bcf,dump,log"/> |
142 </section> | 145 </section> |
146 <output name="out_bcf"> | |
147 <assert_contents> | |
148 <has_size value="1186" delta="10"/> | |
149 </assert_contents> | |
150 </output> | |
151 <output name="out_dump"> | |
152 <assert_contents> | |
153 <has_n_lines n="0"/> | |
154 </assert_contents> | |
155 </output> | |
156 <output name="out_log"> | |
157 <assert_contents> | |
158 <has_text_matching expression=".+Done.+"/> | |
159 </assert_contents> | |
160 </output> | |
143 <output name="out_vcf"> | 161 <output name="out_vcf"> |
144 <assert_contents> | 162 <assert_contents> |
145 <has_size value="3661" delta="10"/> | 163 <has_size value="3661" delta="10"/> |
146 </assert_contents> | |
147 </output> | |
148 <output name="out_bcf"> | |
149 <assert_contents> | |
150 <has_size value="1186" delta="10"/> | |
151 </assert_contents> | |
152 </output> | |
153 <output name="out_dump"> | |
154 <assert_contents> | |
155 <has_n_lines n="0"/> | |
156 </assert_contents> | |
157 </output> | |
158 <output name="out_log"> | |
159 <assert_contents> | |
160 <has_text_matching expression=".+Done.+"/> | |
161 </assert_contents> | 164 </assert_contents> |
162 </output> | 165 </output> |
163 </test> | 166 </test> |
164 <!-- #4 --> | 167 <!-- #4 --> |
165 <test expect_num_outputs="4"> | 168 <test expect_num_outputs="4"> |
166 <param name="samples" value="normal.bam"/> | 169 <param name="input" value="normal.bam"/> |
167 <section name="generic"> | 170 <section name="generic"> |
168 <param name="genome" value="genome.fasta"/> | 171 <param name="genome" value="genome.fasta"/> |
169 <param name="svtype" value="DEL"/> | 172 <param name="svtype" value="DEL"/> |
170 <param name="technology" value="pb"/> | 173 <param name="technology" value="pb"/> |
171 </section> | 174 </section> |
176 <param name="minclip" value="24"/> | 179 <param name="minclip" value="24"/> |
177 <param name="mincliquesize" value="1"/> | 180 <param name="mincliquesize" value="1"/> |
178 <param name="minrefsep" value="24"/> | 181 <param name="minrefsep" value="24"/> |
179 <param name="maxreadsep" value="39"/> | 182 <param name="maxreadsep" value="39"/> |
180 </section> | 183 </section> |
184 <section name="consensus"> | |
185 <param name="maxreads" value="6"/> | |
186 <param name="flanksize" value="399"/> | |
187 <param name="flankquality" value="0.91"/> | |
188 </section> | |
181 <section name="genotyping"> | 189 <section name="genotyping"> |
182 <param name="genoqual" value="4"/> | 190 <param name="genoqual" value="4"/> |
183 </section> | 191 </section> |
184 <section name="oo"> | 192 <section name="oo"> |
185 <param name="out" value="vcf,bcf,dump,log"/> | 193 <param name="out" value="vcf,bcf,dump,log"/> |
187 <output name="out_bcf"> | 195 <output name="out_bcf"> |
188 <assert_contents> | 196 <assert_contents> |
189 <has_size value="1182" delta="10"/> | 197 <has_size value="1182" delta="10"/> |
190 </assert_contents> | 198 </assert_contents> |
191 </output> | 199 </output> |
200 <output name="out_dump"> | |
201 <assert_contents> | |
202 <has_size value="0"/> | |
203 </assert_contents> | |
204 </output> | |
205 <output name="out_log"> | |
206 <assert_contents> | |
207 <has_text_matching expression=".+"/> | |
208 </assert_contents> | |
209 </output> | |
192 <output name="out_vcf"> | 210 <output name="out_vcf"> |
193 <assert_contents> | 211 <assert_contents> |
194 <has_size value="3661" delta="10"/> | 212 <has_size value="3661" delta="10"/> |
195 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | 213 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> |
196 </assert_contents> | 214 </assert_contents> |
197 </output> | 215 </output> |
198 <output name="out_dump"> | |
199 <assert_contents> | |
200 <has_size value="0"/> | |
201 </assert_contents> | |
202 </output> | |
203 <output name="out_log"> | |
204 <assert_contents> | |
205 <has_text_matching expression=".+"/> | |
206 </assert_contents> | |
207 </output> | |
208 </test> | 216 </test> |
209 <!-- #5 --> | 217 <!-- #5 --> |
210 <test expect_num_outputs="1"> | 218 <test expect_num_outputs="1"> |
211 <param name="samples" value="normal.bam"/> | 219 <param name="input" value="normal.bam"/> |
212 <section name="generic"> | 220 <section name="generic"> |
213 <param name="genome" value="genome.fasta"/> | 221 <param name="genome" value="genome.fasta"/> |
214 <param name="svtype" value="INS"/> | 222 <param name="svtype" value="INS"/> |
215 </section> | 223 </section> |
216 <section name="oo"> | 224 <section name="oo"> |
223 </assert_contents> | 231 </assert_contents> |
224 </output> | 232 </output> |
225 </test> | 233 </test> |
226 <!-- #6 --> | 234 <!-- #6 --> |
227 <test expect_num_outputs="1"> | 235 <test expect_num_outputs="1"> |
228 <param name="samples" value="normal.bam"/> | 236 <param name="input" value="normal.bam"/> |
229 <section name="generic"> | 237 <section name="generic"> |
230 <param name="genome" value="genome.fasta"/> | 238 <param name="genome" value="genome.fasta"/> |
231 <param name="svtype" value="DUP"/> | 239 <param name="svtype" value="DUP"/> |
232 </section> | 240 </section> |
233 <section name="oo"> | 241 <section name="oo"> |
239 </assert_contents> | 247 </assert_contents> |
240 </output> | 248 </output> |
241 </test> | 249 </test> |
242 <!-- #7 --> | 250 <!-- #7 --> |
243 <test expect_num_outputs="1"> | 251 <test expect_num_outputs="1"> |
244 <param name="samples" value="normal.bam"/> | 252 <param name="input" value="normal.bam"/> |
245 <section name="generic"> | 253 <section name="generic"> |
246 <param name="genome" value="genome.fasta"/> | 254 <param name="genome" value="genome.fasta"/> |
247 <param name="svtype" value="INV"/> | 255 <param name="svtype" value="INV"/> |
248 </section> | 256 </section> |
249 <section name="oo"> | 257 <section name="oo"> |
255 </assert_contents> | 263 </assert_contents> |
256 </output> | 264 </output> |
257 </test> | 265 </test> |
258 <!-- #8 --> | 266 <!-- #8 --> |
259 <test expect_num_outputs="1"> | 267 <test expect_num_outputs="1"> |
260 <param name="samples" value="normal.bam"/> | 268 <param name="input" value="normal.bam"/> |
261 <section name="generic"> | 269 <section name="generic"> |
262 <param name="genome" value="genome.fasta"/> | 270 <param name="genome" value="genome.fasta"/> |
263 <param name="svtype" value="BND"/> | 271 <param name="svtype" value="BND"/> |
264 </section> | 272 </section> |
265 <section name="oo"> | 273 <section name="oo"> |
277 | 285 |
278 **What it does** | 286 **What it does** |
279 | 287 |
280 @WID@ | 288 @WID@ |
281 | 289 |
282 Delly *long-read (lr)* uses the long-read SV discovery mode. | |
283 | |
284 **Input** | 290 **Input** |
285 | 291 |
286 Delly *long-read (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. | 292 Delly *long-read (lr)* needs a sorted, indexed and duplicate marked BAM file for every input sample. An indexed reference genome is required to identify split-reads. |
287 | 293 |
288 **Output** | 294 **Output** |
289 | 295 |
290 The output is available in BCF and VCF format. Additionally an output file for SV-reads is provided. | 296 The output is available in BCF and VCF format. Additionally an output file for SV-reads and a log file are provided. |
291 | 297 |
292 .. class:: infomark | 298 .. class:: infomark |
293 | 299 |
294 **References** | 300 **References** |
295 | 301 |