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comparison call.xml @ 0:e15927444573 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 07:43:20 +0000
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-1:000000000000 0:e15927444573
1 <?xml version="1.0"?>
2 <tool id="delly_call" name="Delly call" version="@TOOL_VERSION@+galaxy0" profile="18.01">
3 <description>and genotype 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 call
18 ## generic options
19 --svtype $generic.svtype
20 --genome '$generic.genome'
21 #if $generic.exclude
22 --exclude '$generic.exclude'
23 #end if
24 --outfile 'result.bcf'
25 ## discovery options
26 --map-qual $discovery.mapqual
27 --qual-tra $discovery.qualtra
28 --mad-cutoff $discovery.madcutoff
29 --minclip $discovery.minclip
30 --minrefsep $discovery.minrefsep
31 --maxreadsep $discovery.maxreadsep
32 ## genotyping options
33 #if $genotyping.vcffile
34 --vcffile '$genotyping.vcffile'
35 #end if
36 --geno-qual $genotyping.genoqual
37 #if 'dump' in $oo.out
38 --dump 'dump.tsv.gz'
39 #end if
40 ## samples
41 #for $i, $current in enumerate($samples)
42 'sample_${i}.bam'
43 #end for
44
45 ## postprocessing
46 #if 'log' in $oo.out
47 |& tee 'log.txt'
48 #end if
49 #if 'vcf' in $oo.out
50 && test -f 'result.bcf' && bcftools view 'result.bcf' > 'result.vcf' || echo 'No results.'
51 #end if
52 #if 'dump' in $oo.out
53 && test -f 'dump.tsv.gz' && bgzip -d 'dump.tsv.gz' || echo 'No dump file.'
54 #end if
55 ]]></command>
56 <inputs>
57 <expand macro="samples"/>
58 <section name="generic" title="Generic options" expanded="true">
59 <expand macro="svtype"/>
60 <expand macro="genome"/>
61 <expand macro="exclude"/>
62 </section>
63 <section name="discovery" title="Discovery options" expanded="true">
64 <param name="mapqual" type="integer" value="1" label="Set minimum paired-end (PE) mapping quality" help="(--map-qual)"/>
65 <param name="qualtra" type="integer" value="20" label="Set minimum PE quality for translocation" help="(--qual-tra)"/>
66 <param name="madcutoff" type="integer" value="9" label="Set insert size cutoff" help="median+s*MAD, deletions only (--mad-cutoff)"/>
67 <expand macro="minclip"/>
68 <expand macro="minrefsep"/>
69 <expand macro="maxreadsep"/>
70 </section>
71 <section name="genotyping" title="Genotyping options" expanded="true">
72 <expand macro="vcffile"/>
73 <expand macro="genoqual"/>
74 </section>
75 <section name="oo" title="Output options">
76 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
77 <option value="bcf" selected="true">BCF</option>
78 <option value="vcf">VCF</option>
79 <option value="dump">SV-reads (--dump)</option>
80 <option value="log">Log</option>
81 </param>
82 </section>
83 </inputs>
84 <outputs>
85 <expand macro="vcf"/>
86 <expand macro="bcf"/>
87 <expand macro="dump"/>
88 <expand macro="log"/>
89 </outputs>
90 <tests>
91 <!-- no test implemented for parameter vcffile -->
92
93 <!-- #1 default, single -->
94 <test expect_num_outputs="2">
95 <param name="samples" value="normal.bam"/>
96 <section name="generic">
97 <param name="genome" value="genome.fasta"/>
98 </section>
99 <section name="oo">
100 <param name="out" value="vcf,bcf"/>
101 </section>
102 <output name="out_vcf">
103 <assert_contents>
104 <has_size value="3661" delta="10"/>
105 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
106 </assert_contents>
107 </output>
108 <output name="out_bcf">
109 <assert_contents>
110 <has_size value="1184" delta="10"/>
111 </assert_contents>
112 </output>
113 </test>
114 <!-- #2 default, multi; test data to small, results are empty -->
115 <test expect_num_outputs="3">
116 <param name="samples" value="normal.bam,tumor.bam"/>
117 <section name="generic">
118 <param name="genome" value="genome.fasta"/>
119 </section>
120 <section name="oo">
121 <param name="out" value="vcf,bcf,log"/>
122 </section>
123 <output name="out_vcf">
124 <assert_contents>
125 <has_size value="0"/>
126 </assert_contents>
127 </output>
128 <output name="out_bcf">
129 <assert_contents>
130 <has_size value="0"/>
131 </assert_contents>
132 </output>
133 <output name="out_log">
134 <assert_contents>
135 <has_text_matching expression="Sample has not enough data to estimate library parameters.+"/>
136 </assert_contents>
137 </output>
138 </test>
139 <!-- #3; results are empty due to exclude file -->
140 <test expect_num_outputs="4">
141 <param name="samples" value="normal.bam"/>
142 <section name="generic">
143 <param name="genome" value="genome.fasta"/>
144 <param name="exclude" value="exclude.tsv"/>
145 </section>
146 <section name="oo">
147 <param name="out" value="vcf,bcf,dump,log"/>
148 </section>
149 <output name="out_vcf">
150 <assert_contents>
151 <has_size value="0"/>
152 </assert_contents>
153 </output>
154 <output name="out_bcf">
155 <assert_contents>
156 <has_size value="0"/>
157 </assert_contents>
158 </output>
159 <output name="out_dump">
160 <assert_contents>
161 <has_n_lines n="0"/>
162 </assert_contents>
163 </output>
164 <output name="out_log">
165 <assert_contents>
166 <has_text_matching expression="Sample has not enough data to estimate library parameters.+"/>
167 </assert_contents>
168 </output>
169 </test>
170 <!-- #4 -->
171 <test expect_num_outputs="1">
172 <param name="samples" value="normal.bam"/>
173 <section name="generic">
174 <param name="svtype" value="ALL"/>
175 <param name="genome" value="genome.fasta"/>
176 </section>
177 <section name="discovery">
178 <param name="mapqual" value="2"/>
179 <param name="qualtra" value="19"/>
180 <param name="madcutoff" value="8"/>
181 <param name="minclip" value="24"/>
182 <param name="minrefsep" value="24"/>
183 <param name="maxreadsep" value="39"/>
184 </section>
185 <section name="genotyping">
186 <param name="genoqual" value="4"/>
187 </section>
188 <section name="oo">
189 <param name="out" value="vcf"/>
190 </section>
191 <output name="out_vcf">
192 <assert_contents>
193 <has_size value="3661" delta="10"/>
194 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
195 </assert_contents>
196 </output>
197 </test>
198 <!-- #5 -->
199 <test expect_num_outputs="1">
200 <param name="samples" value="normal.bam"/>
201 <section name="generic">
202 <param name="svtype" value="DEL"/>
203 <param name="genome" value="genome.fasta"/>
204 </section>
205 <section name="oo">
206 <param name="out" value="bcf"/>
207 </section>
208 <output name="out_bcf">
209 <assert_contents>
210 <has_size value="1183" delta="10"/>
211 </assert_contents>
212 </output>
213 </test>
214 <!-- #6 -->
215 <test expect_num_outputs="1">
216 <param name="samples" value="normal.bam"/>
217 <section name="generic">
218 <param name="svtype" value="INS"/>
219 <param name="genome" value="genome.fasta"/>
220 </section>
221 <section name="oo">
222 <param name="out" value="dump"/>
223 </section>
224 <output name="out_dump">
225 <assert_contents>
226 <has_size value="0"/>
227 </assert_contents>
228 </output>
229 </test>
230 <!-- #7 -->
231 <test expect_num_outputs="1">
232 <param name="samples" value="normal.bam"/>
233 <section name="generic">
234 <param name="svtype" value="INV"/>
235 <param name="genome" value="genome.fasta"/>
236 </section>
237 <section name="oo">
238 <param name="out" value="log"/>
239 </section>
240 <output name="out_log">
241 <assert_contents>
242 <has_text_matching expression=".+Done.+"/>
243 </assert_contents>
244 </output>
245 </test>
246 <!-- #8 -->
247 <test expect_num_outputs="2">
248 <param name="samples" value="normal.bam"/>
249 <section name="generic">
250 <param name="svtype" value="BND"/>
251 <param name="genome" value="genome.fasta"/>
252 </section>
253 <section name="oo">
254 <param name="out" value="vcf,log"/>
255 </section>
256 <output name="out_vcf">
257 <assert_contents>
258 <has_size value="3661" delta="10"/>
259 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
260 </assert_contents>
261 </output>
262 <output name="out_log">
263 <assert_contents>
264 <has_text_matching expression=".+Done.+"/>
265 </assert_contents>
266 </output>
267 </test>
268 </tests>
269 <help><![CDATA[
270 .. class:: infomark
271
272 **What it does**
273
274 @WID@
275
276 **Input**
277
278 Delly *call* 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.
279
280 **Output**
281
282 The output is available in BCF and VCF format. Additionally a output file for SV-reads is provided.
283
284 .. class:: infomark
285
286 **References**
287
288 @REFERENCES@
289 ]]></help>
290 <expand macro="citations"/>
291 </tool>