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comparison classify.xml @ 0:d3bc6ec7881f 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 14:33:05 +0000
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-1:000000000000 0:d3bc6ec7881f
1 <?xml version="1.0"?>
2 <tool id="delly_classify" name="Delly classify" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
3 <description>somatic or germline copy-number 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 #if $input.is_of_type('vcf')
12 bcftools view -Ob '$input' > 'input.bcf.gz' &&
13 bcftools index 'input.bcf.gz' &&
14 #else
15 ln -s '${input}' 'input.bcf.gz' &&
16 ln -s '${input.metadata.bcf_index}' 'input.bcf.gz.csi' &&
17 #end if
18
19 ## run
20 delly classify
21 ## generic options
22 --filter $sv.mode_cond.mode_sel
23 --outfile 'result.bcf'
24 --minsize $generic.minsize
25 --maxsize $generic.maxsize
26 $generic.pass
27 ## somatic options
28 #if $sv.mode_cond.mode_sel == 'somatic'
29 --samples '$sv.mode_cond.samples'
30 --pgerm $sv.mode_cond.pgerm
31 --cn-offset $sv.mode_cond.cnoffset
32 ## germline options
33 #else if $sv.mode_cond.mode_sel == 'germline'
34 --ploidy $sv.mode_cond.ploidy
35 --qual $sv.mode_cond.qual
36 --maxsd $sv.mode_cond.maxsd
37 #end if
38 ## input
39 'input.bcf.gz'
40
41 ## postprocessing
42 @LOG@
43 @VCF@
44 ]]></command>
45 <inputs>
46 <expand macro="input" format="bcf,vcf" label="Select input file"/>
47 <section name="generic" title="Generic options" expanded="true">
48 <expand macro="minsize" default="1000" label="Set minimum CNV size"/>
49 <expand macro="maxsize" default="500000000" label="Set maximum CNV size"/>
50 <expand macro="pass"/>
51 </section>
52 <section name="sv" title="SV calling options" expanded="true">
53 <conditional name="mode_cond">
54 <param name="mode_sel" type="select" label="Select filter mode" help="(--filter)">
55 <option value="somatic" selected="true">Somatic</option>
56 <option value="germline">Germline</option>
57 </param>
58 <when value="somatic">
59 <expand macro="samples"/>
60 <param argument="--pgerm" type="float" value="0.05" label="Set probability germline"/>
61 <expand macro="cnoffset" default="0.2"/>
62 </when>
63 <when value="germline">
64 <expand macro="ploidy"/>
65 <param argument="--qual" type="integer" value="50" label="Set minimum site quality"/>
66 <param argument="--maxsd" type="float" value="0.15" label="Set maximum population SD"/>
67 </when>
68 </conditional>
69 </section>
70 <section name="oo" title="Output options" expanded="true">
71 <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
72 <option value="bcf" selected="true">BCF</option>
73 <option value="log">Log</option>
74 <option value="vcf">VCF</option>
75 </param>
76 </section>
77 </inputs>
78 <outputs>
79 <expand macro="bcf"/>
80 <expand macro="log"/>
81 <expand macro="vcf"/>
82 </outputs>
83 <tests>
84 <!-- #1 somatic, default -->
85 <test expect_num_outputs="3">
86 <param name="input" value="call_1.bcf.gz"/>
87 <section name="sv">
88 <conditional name="mode_cond">
89 <param name="mode_sel" value="somatic"/>
90 <param name="samples" value="samples.tsv"/>
91 </conditional>
92 </section>
93 <section name="oo">
94 <param name="out" value="bcf,vcf,log"/>
95 </section>
96 <output name="out_bcf">
97 <assert_contents>
98 <has_size value="2322"/>
99 </assert_contents>
100 </output>
101 <output name="out_log">
102 <assert_contents>
103 <has_text_matching expression=".+Done.+"/>
104 </assert_contents>
105 </output>
106 <output name="out_vcf">
107 <assert_contents>
108 <has_size value="7762"/>
109 </assert_contents>
110 </output>
111 </test>
112 <!-- #2 somatic -->
113 <test expect_num_outputs="3">
114 <param name="input" value="call_1.bcf.gz"/>
115 <section name="generic">
116 <param name="minsize" value="1001"/>
117 <param name="maxsize" value="500000001"/>
118 <param name="pass" value="true"/>
119 </section>
120 <section name="sv">
121 <conditional name="mode_cond">
122 <param name="mode_sel" value="somatic"/>
123 <param name="samples" value="samples.tsv"/>
124 <param name="pgerm" value="0.04"/>
125 <param name="cnoffset" value="0.19"/>
126 </conditional>
127 </section>
128 <section name="oo">
129 <param name="out" value="bcf,vcf,log"/>
130 </section>
131 <output name="out_bcf">
132 <assert_contents>
133 <has_size value="2322"/>
134 </assert_contents>
135 </output>
136 <output name="out_log">
137 <assert_contents>
138 <has_text_matching expression=".+Done.+"/>
139 </assert_contents>
140 </output>
141 <output name="out_vcf">
142 <assert_contents>
143 <has_size value="7762"/>
144 </assert_contents>
145 </output>
146 </test>
147 <!-- #3 germline, default -->
148 <test expect_num_outputs="3">
149 <param name="input" value="call_1.bcf.gz"/>
150 <section name="sv">
151 <conditional name="mode_cond">
152 <param name="mode_sel" value="germline"/>
153 </conditional>
154 </section>
155 <section name="oo">
156 <param name="out" value="bcf,vcf,log"/>
157 </section>
158 <output name="out_bcf">
159 <assert_contents>
160 <has_size value="2270"/>
161 </assert_contents>
162 </output>
163 <output name="out_log">
164 <assert_contents>
165 <has_text_matching expression=".+Done.+"/>
166 </assert_contents>
167 </output>
168 <output name="out_vcf">
169 <assert_contents>
170 <has_size value="7665"/>
171 </assert_contents>
172 </output>
173 </test>
174 <!-- #4 germline -->
175 <test expect_num_outputs="3">
176 <param name="input" value="call_1.bcf.gz"/>
177 <section name="sv">
178 <conditional name="mode_cond">
179 <param name="mode_sel" value="germline"/>
180 <param name="ploidy" value="1"/>
181 <param name="qual" value="51"/>
182 <param name="maxsd" value="0.16"/>
183 </conditional>
184 </section>
185 <section name="oo">
186 <param name="out" value="bcf,vcf,log"/>
187 </section>
188 <output name="out_bcf">
189 <assert_contents>
190 <has_size value="2270"/>
191 </assert_contents>
192 </output>
193 <output name="out_log">
194 <assert_contents>
195 <has_text_matching expression=".+Done.+"/>
196 </assert_contents>
197 </output>
198 <output name="out_vcf">
199 <assert_contents>
200 <has_size value="7665"/>
201 </assert_contents>
202 </output>
203 </test>
204 </tests>
205 <help><![CDATA[
206 .. class:: infomark
207
208 **What it does**
209
210 @WID@
211
212 Delly *classify* for somatic or germline copy-number variants.
213
214 **Input**
215
216 Delly *classify* requires an input file in BCF format that can be generated with e.g. Delly *merge*. Additionally a tab-delimited sample description file is required where the first column is the sample id (as in the VCF/BCF file) and the second column is either tumor or control.
217
218 **Output**
219
220 The output is available in BCF and VCF format. Additionally a log file is provided.
221
222 .. class:: infomark
223
224 **References**
225
226 @REFERENCES@
227 ]]></help>
228 <expand macro="citations"/>
229 </tool>