Mercurial > repos > iuc > coverm_contig
comparison coverm_contig.xml @ 4:1dcea261abbe draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5
| author | iuc |
|---|---|
| date | Fri, 18 Aug 2023 09:23:21 +0000 |
| parents | c2a5823e4763 |
| children |
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| 3:c2a5823e4763 | 4:1dcea261abbe |
|---|---|
| 229 </test> | 229 </test> |
| 230 <test expect_num_outputs="1"> | 230 <test expect_num_outputs="1"> |
| 231 <conditional name="mapped"> | 231 <conditional name="mapped"> |
| 232 <param name="mapped" value="not-mapped" /> | 232 <param name="mapped" value="not-mapped" /> |
| 233 <conditional name="mode"> | 233 <conditional name="mode"> |
| 234 <param name="mode" value="individual"/> | |
| 235 <conditional name="read_type"> | |
| 236 <param name="type" value="paired_collection"/> | |
| 237 <param name="paired_reads"> | |
| 238 <collection type="paired"> | |
| 239 <element name="forward" value="reads_for_seq1_and_seq2.1.fq.gz" ftype="fastqsanger.gz"/> | |
| 240 <element name="reverse" value="reads_for_seq1_and_seq2.2.fq.gz" ftype="fastqsanger.gz"/> | |
| 241 </collection> | |
| 242 </param> | |
| 243 </conditional> | |
| 244 <param name="reference" value="7seqs.fna" /> | |
| 245 <param name="sharded" value="" /> | |
| 246 </conditional> | |
| 247 </conditional> | |
| 248 <section name="alignment"> | |
| 249 <param name="min_read_aligned_length" value="0" /> | |
| 250 <param name="min_read_percent_identity" value="0" /> | |
| 251 <param name="min_read_aligned_percent" value="0" /> | |
| 252 <conditional name="proper_pairs_only"> | |
| 253 <param name="proper_pairs_only" value=""/> | |
| 254 </conditional> | |
| 255 <param name="exclude_supplementary" value=""/> | |
| 256 </section> | |
| 257 <section name="cov"> | |
| 258 <param name="methods" value="mean"/> | |
| 259 <param name="trim_min" value="5"/> | |
| 260 <param name="trim_max" value="95"/> | |
| 261 <param name="min_covered_fraction" value="10"/> | |
| 262 <param name="contig_end_exclusion" value="75"/> | |
| 263 </section> | |
| 264 <param name="output_format" value="dense"/> | |
| 265 <output name="output" ftype="tabular"> | |
| 266 <assert_contents> | |
| 267 <has_text text="Contig"/> | |
| 268 <has_text text="Mean"/> | |
| 269 <has_text text="7seqs.fna"/> | |
| 270 <has_text text="genome1~random_sequence_length_11000"/> | |
| 271 <has_text text="genome2~seq1"/> | |
| 272 </assert_contents> | |
| 273 </output> | |
| 274 </test> | |
| 275 <test expect_num_outputs="1"> | |
| 276 <conditional name="mapped"> | |
| 277 <param name="mapped" value="not-mapped" /> | |
| 278 <conditional name="mode"> | |
| 234 <param name="mode" value="co"/> | 279 <param name="mode" value="co"/> |
| 235 <conditional name="read_type"> | 280 <conditional name="read_type"> |
| 236 <param name="type" value="single"/> | 281 <param name="type" value="single"/> |
| 237 <param name="single" value="bad_reads.interleaved.fq"/> | 282 <param name="single" value="bad_reads.interleaved.fq"/> |
| 238 </conditional> | 283 </conditional> |