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comparison lr.xml @ 2:eb4284f666b1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a"
author iuc
date Fri, 22 Jan 2021 14:29:56 +0000
parents fba03b9b3b16
children 0e56998aebc6
comparison
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1:fba03b9b3b16 2:eb4284f666b1
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&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/> 107 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;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&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/> 213 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;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