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comparison lr.xml @ 5:0564602cd4df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
author iuc
date Mon, 27 Jun 2022 18:14:26 +0000
parents 0e56998aebc6
children d00d96187fd2
comparison
equal deleted inserted replaced
4:790d4c1f2ea0 5:0564602cd4df
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <expand macro="version_command"/> 9 <expand macro="version_command"/>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 ## initialize 11 ## initialize
12 @BAM@ 12 @BAM@
13 13 @FASTA@
14 ## run 14 ## run
15 delly lr 15 delly lr
16 ## generic options 16 ## generic options
17 --svtype $generic.svtype 17 --svtype $generic.svtype
18 --technology $generic.technology 18 --technology $generic.technology
19 --genome '$generic.genome' 19 --genome genome.fa
20 #if $generic.exclude 20 #if $generic.exclude
21 --exclude '$generic.exclude' 21 --exclude '$generic.exclude'
22 #end if 22 #end if
23 --outfile 'result.bcf' 23 --outfile 'result.bcf'
24 ## discovery options 24 ## discovery options
97 <section name="oo"> 97 <section name="oo">
98 <param name="out" value="vcf,bcf"/> 98 <param name="out" value="vcf,bcf"/>
99 </section> 99 </section>
100 <output name="out_bcf"> 100 <output name="out_bcf">
101 <assert_contents> 101 <assert_contents>
102 <has_size value="1184" delta="10"/> 102 <has_size value="1127" delta="10"/>
103 </assert_contents> 103 </assert_contents>
104 </output> 104 </output>
105 <output name="out_vcf"> 105 <output name="out_vcf">
106 <assert_contents> 106 <assert_contents>
107 <has_size value="3661" delta="10"/> 107 <has_n_lines n="46"/>
108 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/> 108 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
109 </assert_contents> 109 </assert_contents>
110 </output> 110 </output>
111 </test> 111 </test>
112 <!-- #2 default, multi; test data to small, results are empty --> 112 <!-- #2 default, multi; test data to small, results are empty -->
118 <section name="oo"> 118 <section name="oo">
119 <param name="out" value="vcf,bcf,log"/> 119 <param name="out" value="vcf,bcf,log"/>
120 </section> 120 </section>
121 <output name="out_bcf"> 121 <output name="out_bcf">
122 <assert_contents> 122 <assert_contents>
123 <has_size value="1189" delta="10"/> 123 <has_size value="1131" delta="10"/>
124 </assert_contents> 124 </assert_contents>
125 </output> 125 </output>
126 <output name="out_log"> 126 <output name="out_log">
127 <assert_contents> 127 <assert_contents>
128 <has_text_matching expression=".+Done.+"/> 128 <has_text_matching expression=".+Done.+"/>
129 </assert_contents> 129 </assert_contents>
130 </output> 130 </output>
131 <output name="out_vcf"> 131 <output name="out_vcf">
132 <assert_contents> 132 <assert_contents>
133 <has_size value="3667" delta="10"/> 133 <has_n_lines valuen="42"/>
134 </assert_contents> 134 </assert_contents>
135 </output> 135 </output>
136 </test> 136 </test>
137 <!-- #3 --> 137 <!-- #3 -->
138 <test expect_num_outputs="4"> 138 <test expect_num_outputs="4">
144 <section name="oo"> 144 <section name="oo">
145 <param name="out" value="vcf,bcf,dump,log"/> 145 <param name="out" value="vcf,bcf,dump,log"/>
146 </section> 146 </section>
147 <output name="out_bcf"> 147 <output name="out_bcf">
148 <assert_contents> 148 <assert_contents>
149 <has_size value="1186" delta="10"/> 149 <has_size value="1127" delta="10"/>
150 </assert_contents> 150 </assert_contents>
151 </output> 151 </output>
152 <output name="out_dump"> 152 <output name="out_dump">
153 <assert_contents> 153 <assert_contents>
154 <has_n_lines n="0"/> 154 <has_n_lines n="0"/>
159 <has_text_matching expression=".+Done.+"/> 159 <has_text_matching expression=".+Done.+"/>
160 </assert_contents> 160 </assert_contents>
161 </output> 161 </output>
162 <output name="out_vcf"> 162 <output name="out_vcf">
163 <assert_contents> 163 <assert_contents>
164 <has_size value="3661" delta="10"/> 164 <has_n_lines n="46"/>
165 </assert_contents> 165 </assert_contents>
166 </output> 166 </output>
167 </test> 167 </test>
168 <!-- #4 --> 168 <!-- #4 -->
169 <test expect_num_outputs="4"> 169 <test expect_num_outputs="4">
193 <section name="oo"> 193 <section name="oo">
194 <param name="out" value="vcf,bcf,dump,log"/> 194 <param name="out" value="vcf,bcf,dump,log"/>
195 </section> 195 </section>
196 <output name="out_bcf"> 196 <output name="out_bcf">
197 <assert_contents> 197 <assert_contents>
198 <has_size value="1182" delta="10"/> 198 <has_size value="1127" delta="10"/>
199 </assert_contents> 199 </assert_contents>
200 </output> 200 </output>
201 <output name="out_dump"> 201 <output name="out_dump">
202 <assert_contents> 202 <assert_contents>
203 <has_size value="0"/> 203 <has_size value="0"/>
208 <has_text_matching expression=".+"/> 208 <has_text_matching expression=".+"/>
209 </assert_contents> 209 </assert_contents>
210 </output> 210 </output>
211 <output name="out_vcf"> 211 <output name="out_vcf">
212 <assert_contents> 212 <assert_contents>
213 <has_size value="3661" delta="10"/> 213 <has_n_lines n="46"/>
214 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/> 214 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
215 </assert_contents> 215 </assert_contents>
216 </output> 216 </output>
217 </test> 217 </test>
218 <!-- #5 --> 218 <!-- #5 -->
225 <section name="oo"> 225 <section name="oo">
226 <param name="out" value="vcf"/> 226 <param name="out" value="vcf"/>
227 </section> 227 </section>
228 <output name="out_vcf"> 228 <output name="out_vcf">
229 <assert_contents> 229 <assert_contents>
230 <has_size value="3661" delta="10"/> 230 <has_n_lines n="46"/>
231 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/> 231 <has_line line="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO&#009;FORMAT&#009;normal"/>
232 </assert_contents> 232 </assert_contents>
233 </output> 233 </output>
234 </test> 234 </test>
235 <!-- #6 --> 235 <!-- #6 -->
242 <section name="oo"> 242 <section name="oo">
243 <param name="out" value="bcf"/> 243 <param name="out" value="bcf"/>
244 </section> 244 </section>
245 <output name="out_bcf"> 245 <output name="out_bcf">
246 <assert_contents> 246 <assert_contents>
247 <has_size value="1182" delta="10"/> 247 <has_size value="1127" delta="10"/>
248 </assert_contents> 248 </assert_contents>
249 </output> 249 </output>
250 </test> 250 </test>
251 <!-- #7 --> 251 <!-- #7 -->
252 <test expect_num_outputs="1"> 252 <test expect_num_outputs="1">