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comparison filter.xml @ 2:6184cfc70e28 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 14:32:03 +0000
parents 9919057a466c
children d2590fe6793f
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1:9919057a466c 2:6184cfc70e28
6 </macros> 6 </macros>
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 #if $samples.is_of_type('vcf') 11 #if $input.is_of_type('vcf')
12 bcftools view -Ob '$samples' > 'sample.bcf.gz' && 12 bcftools view -Ob '$input' > 'input.bcf.gz' &&
13 bcftools index 'sample.bcf.gz' && 13 bcftools index 'input.bcf.gz' &&
14 #else 14 #else
15 ln -s '${samples}' 'sample.bcf.gz' && 15 ln -s '${input}' 'input.bcf.gz' &&
16 ln -s '${samples.metadata.bcf_index}' 'sample.bcf.gz.csi' && 16 ln -s '${input.metadata.bcf_index}' 'input.bcf.gz.csi' &&
17 #end if 17 #end if
18 18
19 ## run 19 ## run
20 delly filter 20 delly filter
21 ## generic options 21 ## generic options
29 ## somatic options 29 ## somatic options
30 #if $sv.mode_cond.mode_sel == 'somatic' 30 #if $sv.mode_cond.mode_sel == 'somatic'
31 --samples '$sv.mode_cond.samples' 31 --samples '$sv.mode_cond.samples'
32 --coverage $sv.mode_cond.coverage 32 --coverage $sv.mode_cond.coverage
33 --controlcontamination $sv.mode_cond.controlcontamination 33 --controlcontamination $sv.mode_cond.controlcontamination
34 #end if
35 ## germline options 34 ## germline options
36 #if $sv.mode_cond.mode_sel == 'germline' 35 #else if $sv.mode_cond.mode_sel == 'germline'
37 --gq $sv.mode_cond.gq 36 --gq $sv.mode_cond.gq
38 --rddel $sv.mode_cond.rddel 37 --rddel $sv.mode_cond.rddel
39 --rddup $sv.mode_cond.rddup 38 --rddup $sv.mode_cond.rddup
40 #end if 39 #end if
41 ## samples 40 ## input
42 'sample.bcf.gz' ## input 41 'input.bcf.gz'
43 42
44 ## postprocessing 43 ## postprocessing
45 @LOG@ 44 @LOG@
46 @VCF@ 45 @VCF@
47 ]]></command> 46 ]]></command>
48 <inputs> 47 <inputs>
49 <expand macro="samples" format="bcf,vcf" multiple="false" label="Select file"/> 48 <expand macro="input" format="bcf,vcf" label="Select input file"/>
50 <section name="generic" title="Generic options" expanded="true"> 49 <section name="generic" title="Generic options" expanded="true">
51 <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/> 50 <param argument="--altaf" type="float" value="0.2" min="0.0" max="1.0" label="Set minimum fractional ALT support"/>
52 <expand macro="minsize"/> 51 <expand macro="minsize" default="0" label="Set minimum SV size"/>
53 <expand macro="maxsize" default="500000000"/> 52 <expand macro="maxsize" default="500000000" label="Set maximum SV size"/>
54 <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/> 53 <param argument="--ratiogeno" type="float" value="0.75" min="0.0" max="1.0" label="Set minimum fraction of genotyped samples"/>
55 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/> 54 <param argument="--pass" type="boolean" truevalue="--pass" falsevalue="" label="Filter sites for PASS?"/>
56 </section> 55 </section>
57 <section name="sv" title="SV calling options" expanded="true"> 56 <section name="sv" title="SV calling options" expanded="true">
58 <conditional name="mode_cond"> 57 <conditional name="mode_cond">
59 <param argument="mode_sel" type="select" label="Select filter mode"> 58 <param name="mode_sel" type="select" label="Select filter mode" help="(--filter)">
60 <option value="somatic" selected="true">Somatic</option> 59 <option value="somatic" selected="true">Somatic</option>
61 <option value="germline">Germline</option> 60 <option value="germline">Germline</option>
62 </param> 61 </param>
63 <when value="somatic"> 62 <when value="somatic">
64 <param argument="--samples" type="data" format="tabular" label="Select sample file" help="Two-column sample file listing sample name and tumor or control."/> 63 <expand macro="samples"/>
65 <param argument="--coverage" type="integer" value="10" label="Set minimum coverage in tumor."/> 64 <expand macro="coverage" label="Set minimum coverage in tumor"/>
66 <param argument="--controlcontamination" type="float" value="0.0" min="0.0" max="1.0" label="Set maximum fractional ALT support in control"/> 65 <param argument="--controlcontamination" type="float" value="0.0" min="0.0" max="1.0" label="Set maximum fractional ALT support in control"/>
67 </when> 66 </when>
68 <when value="germline"> 67 <when value="germline">
69 <param argument="--gq" type="integer" value="15" label="Set minimum median GQ for carriers and non-carriers"/> 68 <param argument="--gq" type="integer" value="15" label="Set minimum median GQ for carriers and non-carriers"/>
70 <param argument="--rddel" type="float" value="0.8" label="Set maximum read-depth ratio of carrier vs. non-carrier for a deletion"/> 69 <param argument="--rddel" type="float" value="0.8" label="Set maximum read-depth ratio of carrier vs. non-carrier for a deletion"/>
71 <param argument="--rddup" type="float" value="1.2" label="Set minimum read-depth ratio of carrier vs. non-carrier for a duplication"/> 70 <param argument="--rddup" type="float" value="1.2" label="Set minimum read-depth ratio of carrier vs. non-carrier for a duplication"/>
72 </when> 71 </when>
73 </conditional> 72 </conditional>
74 </section> 73 </section>
75 <section name="oo" title="Output options"> 74 <section name="oo" title="Output options" expanded="true">
76 <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)">
77 <option value="bcf" selected="true">BCF</option> 76 <option value="bcf" selected="true">BCF</option>
77 <option value="log">Log</option>
78 <option value="vcf">VCF</option> 78 <option value="vcf">VCF</option>
79 <option value="log">Log</option>
80 </param> 79 </param>
81 </section> 80 </section>
82 </inputs> 81 </inputs>
83 <outputs> 82 <outputs>
84 <expand macro="vcf"/>
85 <expand macro="bcf"/> 83 <expand macro="bcf"/>
86 <expand macro="log"/> 84 <expand macro="log"/>
85 <expand macro="vcf"/>
87 </outputs> 86 </outputs>
88 <tests> 87 <tests>
89 <!-- #1 default, somatic, bcf --> 88 <!-- #1 default, somatic, bcf -->
90 <test expect_num_outputs="2"> 89 <test expect_num_outputs="2">
91 <param name="samples" value="call_1.bcf.gz"/> 90 <param name="input" value="call_1.bcf.gz"/>
92 <section name="sv"> 91 <section name="sv">
93 <conditional name="mode_cond"> 92 <conditional name="mode_cond">
94 <param name="mode_sel" value="somatic"/> 93 <param name="mode_sel" value="somatic"/>
95 <param name="samples" value="samples.tsv"/> 94 <param name="samples" value="samples.tsv"/>
96 </conditional> 95 </conditional>
111 </assert_contents> 110 </assert_contents>
112 </output> 111 </output>
113 </test> 112 </test>
114 <!-- #2 somatic, bcf --> 113 <!-- #2 somatic, bcf -->
115 <test expect_num_outputs="3"> 114 <test expect_num_outputs="3">
116 <param name="samples" value="call_1.bcf.gz"/> 115 <param name="input" value="call_1.bcf.gz"/>
117 <section name="generic"> 116 <section name="generic">
118 <param name="altaf" value="0.3"/> 117 <param name="altaf" value="0.3"/>
119 <param name="minsize" value="1"/> 118 <param name="minsize" value="1"/>
120 <param name="maxsize" value="500000001"/> 119 <param name="maxsize" value="500000001"/>
121 <param name="ratiogeno" value="0.76"/> 120 <param name="ratiogeno" value="0.76"/>
135 <output name="out_bcf"> 134 <output name="out_bcf">
136 <assert_contents> 135 <assert_contents>
137 <has_size value="2281" delta="10"/> 136 <has_size value="2281" delta="10"/>
138 </assert_contents> 137 </assert_contents>
139 </output> 138 </output>
139 <output name="out_log">
140 <assert_contents>
141 <has_text_matching expression=".+Done\."/>
142 </assert_contents>
143 </output>
140 <output name="out_vcf"> 144 <output name="out_vcf">
141 <assert_contents> 145 <assert_contents>
142 <has_n_lines n="140"/> 146 <has_n_lines n="140"/>
143 <has_line line="##fileformat=VCFv4.2"/> 147 <has_line line="##fileformat=VCFv4.2"/>
144 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;NORMAL&#009;TUMOR"/> 148 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;NORMAL&#009;TUMOR"/>
145 </assert_contents>
146 </output>
147 <output name="out_log">
148 <assert_contents>
149 <has_text_matching expression=".+Done\."/>
150 </assert_contents> 149 </assert_contents>
151 </output> 150 </output>
152 </test> 151 </test>
153 <!-- #3 default, germline, bcf --> 152 <!-- #3 default, germline, bcf -->
154 <test expect_num_outputs="2"> 153 <test expect_num_outputs="2">
155 <param name="samples" value="call_1.bcf.gz"/> 154 <param name="input" value="call_1.bcf.gz"/>
156 <section name="sv"> 155 <section name="sv">
157 <conditional name="mode_cond"> 156 <conditional name="mode_cond">
158 <param name="mode_sel" value="germline"/> 157 <param name="mode_sel" value="germline"/>
159 </conditional> 158 </conditional>
160 </section> 159 </section>
174 </assert_contents> 173 </assert_contents>
175 </output> 174 </output>
176 </test> 175 </test>
177 <!-- #4 germline, bcf --> 176 <!-- #4 germline, bcf -->
178 <test expect_num_outputs="3"> 177 <test expect_num_outputs="3">
179 <param name="samples" value="call_1.bcf.gz"/> 178 <param name="input" value="call_1.bcf.gz"/>
180 <section name="generic"> 179 <section name="generic">
181 <param name="altaf" value="0.1"/> 180 <param name="altaf" value="0.1"/>
182 <param name="minsize" value="1"/> 181 <param name="minsize" value="1"/>
183 <param name="maxsize" value="500000001"/> 182 <param name="maxsize" value="500000001"/>
184 <param name="ratiogeno" value="0.76"/> 183 <param name="ratiogeno" value="0.76"/>
198 <output name="out_bcf"> 197 <output name="out_bcf">
199 <assert_contents> 198 <assert_contents>
200 <has_size value="2264" delta="10"/> 199 <has_size value="2264" delta="10"/>
201 </assert_contents> 200 </assert_contents>
202 </output> 201 </output>
202 <output name="out_log">
203 <assert_contents>
204 <has_text_matching expression=".+Done\."/>
205 </assert_contents>
206 </output>
203 <output name="out_vcf"> 207 <output name="out_vcf">
204 <assert_contents> 208 <assert_contents>
205 <has_n_lines n="139"/> 209 <has_n_lines n="139"/>
206 <has_line line="##fileformat=VCFv4.2"/> 210 <has_line line="##fileformat=VCFv4.2"/>
207 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;NORMAL&#009;TUMOR"/> 211 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;NORMAL&#009;TUMOR"/>
208 </assert_contents>
209 </output>
210 <output name="out_log">
211 <assert_contents>
212 <has_text_matching expression=".+Done\."/>
213 </assert_contents> 212 </assert_contents>
214 </output> 213 </output>
215 </test> 214 </test>
216 <!-- #5 default, somatic, vcf --> 215 <!-- #5 default, somatic, vcf -->
217 <test expect_num_outputs="2"> 216 <test expect_num_outputs="2">
218 <param name="samples" value="call_1.vcf.gz"/> 217 <param name="input" value="call_1.vcf.gz"/>
219 <section name="sv"> 218 <section name="sv">
220 <conditional name="mode_cond"> 219 <conditional name="mode_cond">
221 <param name="mode_sel" value="somatic"/> 220 <param name="mode_sel" value="somatic"/>
222 <param name="samples" value="samples.tsv"/> 221 <param name="samples" value="samples.tsv"/>
223 </conditional> 222 </conditional>
225 <section name="oo"> 224 <section name="oo">
226 <param name="out" value="vcf,bcf"/> 225 <param name="out" value="vcf,bcf"/>
227 </section> 226 </section>
228 <output name="out_bcf"> 227 <output name="out_bcf">
229 <assert_contents> 228 <assert_contents>
230 <has_size value="2440" delta="10"/> 229 <has_size value="2451" delta="10"/>
231 </assert_contents> 230 </assert_contents>
232 </output> 231 </output>
233 <output name="out_vcf"> 232 <output name="out_vcf">
234 <assert_contents> 233 <assert_contents>
235 <has_n_lines n="142"/> 234 <has_n_lines n="142"/>
244 243
245 **What it does** 244 **What it does**
246 245
247 @WID@ 246 @WID@
248 247
249 Delly *filter* contains workflows for germline and somatic SV calling.
250
251 **Input** 248 **Input**
252 249
253 *Somatic* filtering requires a called SV input with at least one tumor sample and a matched control sample. In addition, a tab-delimited sample description needs to be provided, in which the first column holds the sample ids (as found in the VCF/BCF input) and the second column specifies either tumor or control. 250 *Somatic* filtering requires a called SV input with at least one tumor sample and a matched control sample. In addition, a tab-delimited sample description needs to be provided, in which the first column holds the sample ids (as found in the VCF/BCF input) and the second column specifies either tumor or control.
254 251
255 *Germline* SV calling is done by sample for high-coverage genomes or in small batches for low-coverage genomes. 252 *Germline* SV calling is done by sample for high-coverage genomes or in small batches for low-coverage genomes.
256 253
257 **Output** 254 **Output**
258 255
259 The output is available in BCF and VCF format. 256 The output is available in BCF and VCF format. Additionally a log file is provided.
260 257
261 .. class:: infomark 258 .. class:: infomark
262 259
263 **References** 260 **References**
264 261