Mercurial > repos > iuc > delly_call
comparison call.xml @ 5:29f28384af45 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
| author | iuc |
|---|---|
| date | Mon, 27 Jun 2022 18:13:53 +0000 |
| parents | f0a5257823ba |
| children |
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| 4:4869d7517a51 | 5:29f28384af45 |
|---|---|
| 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 call | 15 delly call |
| 16 ## generic options | 16 ## generic options |
| 17 --svtype $generic.svtype | 17 --svtype $generic.svtype |
| 18 --genome '$generic.genome' | 18 --genome genome.fa |
| 19 #if $generic.exclude | 19 #if $generic.exclude |
| 20 --exclude '$generic.exclude' | 20 --exclude '$generic.exclude' |
| 21 #end if | 21 #end if |
| 22 --outfile 'result.bcf' | 22 --outfile 'result.bcf' |
| 23 ## discovery options | 23 ## discovery options |
| 93 <section name="oo"> | 93 <section name="oo"> |
| 94 <param name="out" value="vcf,bcf"/> | 94 <param name="out" value="vcf,bcf"/> |
| 95 </section> | 95 </section> |
| 96 <output name="out_bcf"> | 96 <output name="out_bcf"> |
| 97 <assert_contents> | 97 <assert_contents> |
| 98 <has_size value="1184" delta="10"/> | 98 <has_size value="1127" delta="10"/> |
| 99 </assert_contents> | 99 </assert_contents> |
| 100 </output> | 100 </output> |
| 101 <output name="out_vcf"> | 101 <output name="out_vcf"> |
| 102 <assert_contents> | 102 <assert_contents> |
| 103 <has_size value="3661" delta="10"/> | 103 <has_n_lines n="46"/> |
| 104 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | 104 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> |
| 105 </assert_contents> | 105 </assert_contents> |
| 106 </output> | 106 </output> |
| 107 </test> | 107 </test> |
| 108 <!-- #2 default, multi; test data to small, results are empty --> | 108 <!-- #2 default, multi; test data to small, results are empty --> |
| 183 <section name="oo"> | 183 <section name="oo"> |
| 184 <param name="out" value="vcf"/> | 184 <param name="out" value="vcf"/> |
| 185 </section> | 185 </section> |
| 186 <output name="out_vcf"> | 186 <output name="out_vcf"> |
| 187 <assert_contents> | 187 <assert_contents> |
| 188 <has_size value="3661" delta="10"/> | 188 <has_n_lines n="46"/> |
| 189 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | 189 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> |
| 190 </assert_contents> | 190 </assert_contents> |
| 191 </output> | 191 </output> |
| 192 </test> | 192 </test> |
| 193 <!-- #5 --> | 193 <!-- #5 --> |
| 200 <section name="oo"> | 200 <section name="oo"> |
| 201 <param name="out" value="bcf"/> | 201 <param name="out" value="bcf"/> |
| 202 </section> | 202 </section> |
| 203 <output name="out_bcf"> | 203 <output name="out_bcf"> |
| 204 <assert_contents> | 204 <assert_contents> |
| 205 <has_size value="1183" delta="10"/> | 205 <has_size value="1127" delta="10"/> |
| 206 </assert_contents> | 206 </assert_contents> |
| 207 </output> | 207 </output> |
| 208 </test> | 208 </test> |
| 209 <!-- #6 --> | 209 <!-- #6 --> |
| 210 <test expect_num_outputs="1"> | 210 <test expect_num_outputs="1"> |
| 248 <section name="oo"> | 248 <section name="oo"> |
| 249 <param name="out" value="vcf,log"/> | 249 <param name="out" value="vcf,log"/> |
| 250 </section> | 250 </section> |
| 251 <output name="out_vcf"> | 251 <output name="out_vcf"> |
| 252 <assert_contents> | 252 <assert_contents> |
| 253 <has_size value="3661" delta="10"/> | 253 <has_n_lines n="46"/> |
| 254 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> | 254 <has_line line="#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	normal"/> |
| 255 </assert_contents> | 255 </assert_contents> |
| 256 </output> | 256 </output> |
| 257 <output name="out_log"> | 257 <output name="out_log"> |
| 258 <assert_contents> | 258 <assert_contents> |