Mercurial > repos > iuc > delly_lr
comparison lr.xml @ 4:7bd397ff21a2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
| author | iuc |
|---|---|
| date | Mon, 27 Jun 2022 18:17:41 +0000 |
| parents | d30785dbe6b7 |
| children | 97f649646cc1 |
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| 3:d30785dbe6b7 | 4:7bd397ff21a2 |
|---|---|
| 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	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | 108 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	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	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | 214 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	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	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | 231 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	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"> |