Mercurial > repos > iuc > unicycler
comparison unicycler.xml @ 8:9e3e80cc4ad4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit d7f4eb848136b02ae1cf121a5cfb2e6175d35406"
| author | iuc |
|---|---|
| date | Wed, 18 Nov 2020 20:26:04 +0000 |
| parents | 88c240872a65 |
| children | 6e26c9afd301 |
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| 7:88c240872a65 | 8:9e3e80cc4ad4 |
|---|---|
| 1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0"> | 1 <tool id="unicycler" name="Create assemblies with Unicycler" version="@VERSION@.0" profile="20.09"> |
| 2 <macros> | 2 <macros> |
| 3 <token name="@VERSION@">0.4.8</token> | 3 <token name="@VERSION@">0.4.8</token> |
| 4 </macros> | 4 </macros> |
| 5 <edam_topics> | 5 <edam_topics> |
| 6 <edam_topic>topic_0196</edam_topic> | 6 <edam_topic>topic_0196</edam_topic> |
| 202 <param argument="--low_score" optional="true" type="integer" value="" | 202 <param argument="--low_score" optional="true" type="integer" value="" |
| 203 label="Score threshold - alignments below this are considered poor" help="default = set automatically"/> | 203 label="Score threshold - alignments below this are considered poor" help="default = set automatically"/> |
| 204 </section> | 204 </section> |
| 205 </inputs> | 205 </inputs> |
| 206 <outputs> | 206 <outputs> |
| 207 <data name="assembly_graph" format="tabular" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> | 207 <data name="assembly_graph" format="gfa1" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" /> |
| 208 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> | 208 <data name="assembly" format="fasta" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/> |
| 209 </outputs> | 209 </outputs> |
| 210 <tests> | 210 <tests> |
| 211 <test> | 211 <test> |
| 212 <conditional name="paired_unpaired"> | 212 <conditional name="paired_unpaired"> |
| 238 <param name="min_dead_end_size" value="1000"/> | 238 <param name="min_dead_end_size" value="1000"/> |
| 239 </section> | 239 </section> |
| 240 <section name="lr_align"> | 240 <section name="lr_align"> |
| 241 <param name="scores" value="3,-6,-5,-2"/> | 241 <param name="scores" value="3,-6,-5,-2"/> |
| 242 </section> | 242 </section> |
| 243 <output name="assembly_graph" ftype="tabular"> | 243 <output name="assembly_graph" ftype="gfa1"> |
| 244 <assert_contents> | 244 <assert_contents> |
| 245 <has_text text="TATCTGTTACTGAGAAGTTAATGGATGAATTGGCAC"/> | 245 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
| 246 </assert_contents> | 246 </assert_contents> |
| 247 </output> | 247 </output> |
| 248 <output name="assembly" ftype="fasta"> | 248 <output name="assembly" ftype="fasta"> |
| 249 <assert_contents> | 249 <assert_contents> |
| 250 <has_text text="length=5386" /> | 250 <has_text text="length=5386" /> |
| 293 <param name="min_dead_end_size" value="1000"/> | 293 <param name="min_dead_end_size" value="1000"/> |
| 294 </section> | 294 </section> |
| 295 <section name="lr_align"> | 295 <section name="lr_align"> |
| 296 <param name="scores" value="3,-6,-5,-2"/> | 296 <param name="scores" value="3,-6,-5,-2"/> |
| 297 </section> | 297 </section> |
| 298 <output name="assembly_graph" ftype="tabular"> | 298 <output name="assembly_graph" ftype="gfa1"> |
| 299 <assert_contents> | 299 <assert_contents> |
| 300 <has_text text="TATCTGTTACTGAGAAGTTAATGGATGAATTGGCAC" /> | 300 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
| 301 </assert_contents> | 301 </assert_contents> |
| 302 </output> | 302 </output> |
| 303 <output name="assembly" ftype="fasta"> | 303 <output name="assembly" ftype="fasta"> |
| 304 <assert_contents> | 304 <assert_contents> |
| 305 <has_text text="length=5386" /> | 305 <has_text text="length=5386" /> |
| 340 <param name="min_dead_end_size" value="1000"/> | 340 <param name="min_dead_end_size" value="1000"/> |
| 341 </section> | 341 </section> |
| 342 <section name="lr_align"> | 342 <section name="lr_align"> |
| 343 <param name="scores" value="3,-6,-5,-2"/> | 343 <param name="scores" value="3,-6,-5,-2"/> |
| 344 </section> | 344 </section> |
| 345 <output name="assembly_graph" ftype="tabular"> | 345 <output name="assembly_graph" ftype="gfa1"> |
| 346 <assert_contents> | 346 <assert_contents> |
| 347 <has_text text="TATCTGTTACTGAGAAGTTAATGGATGAATTGGCAC" /> | 347 <has_line_matching expression="S\t1\t[ATCG]{5386,5386}\tLN:i:5386\tdp:f:1.0"/> |
| 348 </assert_contents> | 348 </assert_contents> |
| 349 </output> | 349 </output> |
| 350 <output name="assembly" ftype="fasta"> | 350 <output name="assembly" ftype="fasta"> |
| 351 <assert_contents> | 351 <assert_contents> |
| 352 <has_text text="length=5386" /> | 352 <has_text text="length=5386" /> |
| 360 <param name="min_anchor_seg_len" value="10"/> | 360 <param name="min_anchor_seg_len" value="10"/> |
| 361 <section name="spades"> | 361 <section name="spades"> |
| 362 <param name="kmers" value="21,23"/> | 362 <param name="kmers" value="21,23"/> |
| 363 </section> | 363 </section> |
| 364 <param name="long" value="only_long.fasta" ftype="fasta" /> | 364 <param name="long" value="only_long.fasta" ftype="fasta" /> |
| 365 <output name="assembly_graph" ftype="tabular"> | 365 <output name="assembly_graph" ftype="gfa1"> |
| 366 <assert_contents> | 366 <assert_contents> |
| 367 <has_text text="S" /> | 367 <has_text text="S" /> |
| 368 </assert_contents> | 368 </assert_contents> |
| 369 </output> | 369 </output> |
| 370 <output name="assembly" ftype="fasta"> | 370 <output name="assembly" ftype="fasta"> |