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comparison lr.xml @ 0:c8bf8a743109 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 86ada42b811af0262618636f2d8d1788274f9884"
author iuc
date Mon, 28 Sep 2020 07:43:50 +0000
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children fba03b9b3b16
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-1:000000000000 0:c8bf8a743109
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&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;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&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;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&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;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>