Mercurial > repos > iuc > busco
comparison busco.xml @ 18:94170eee0ad8 draft
planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
| author | iuc |
|---|---|
| date | Fri, 14 Apr 2023 08:13:46 +0000 |
| parents | e824f5d958d0 |
| children | 2a5b8b9936bf |
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| 17:e824f5d958d0 | 18:94170eee0ad8 |
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| 28 | 28 |
| 29 #end if | 29 #end if |
| 30 | 30 |
| 31 busco | 31 busco |
| 32 --in '${input}' | 32 --in '${input}' |
| 33 --update-data | |
| 34 --mode '${busco_mode.mode}' | 33 --mode '${busco_mode.mode}' |
| 35 --out busco_galaxy | 34 --out busco_galaxy |
| 36 --cpu \${GALAXY_SLOTS:-4} | 35 --cpu \${GALAXY_SLOTS:-4} |
| 37 --evalue ${adv.evalue} | 36 --evalue ${adv.evalue} |
| 38 --limit ${adv.limit} | 37 --limit ${adv.limit} |
| 39 | 38 |
| 39 #if $lineage_conditional.selector == 'cached': | |
| 40 --offline | |
| 41 --download_path $lineage_conditional.cached_db.fields.path | |
| 42 #else | |
| 43 --update-data | |
| 44 #end if | |
| 45 | |
| 40 #if $lineage.lineage_mode == "auto_detect": | 46 #if $lineage.lineage_mode == "auto_detect": |
| 41 $lineage.auto_lineage | 47 $lineage.auto_lineage |
| 42 #else if $lineage.lineage_mode == "select_lineage": | 48 #else if $lineage.lineage_mode == "select_lineage": |
| 43 --lineage_dataset '${lineage.lineage_dataset}' | 49 --lineage_dataset '${lineage.lineage_dataset}' |
| 44 #end if | 50 #end if |
| 73 #end if | 79 #end if |
| 74 | 80 |
| 75 ]]> </command> | 81 ]]> </command> |
| 76 <inputs> | 82 <inputs> |
| 77 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." /> | 83 <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." /> |
| 84 <conditional name="lineage_conditional"> | |
| 85 <param name="selector" type="select" label="Lineage data source"> | |
| 86 <option value="download">Download lineage data</option> | |
| 87 <option value="cached">Use cached lineage data</option> | |
| 88 </param> | |
| 89 <when value="cached"> | |
| 90 <param name="cached_db" label="Cached database with lineage" type="select"> | |
| 91 <options from_data_table="busco_database"> | |
| 92 <validator message="No BUSCO database is available" type="no_options" /> | |
| 93 </options> | |
| 94 </param> | |
| 95 </when> | |
| 96 <when value="download"/> | |
| 97 </conditional> | |
| 78 <conditional name="busco_mode"> | 98 <conditional name="busco_mode"> |
| 79 <param argument="--mode" type="select" label="Mode"> | 99 <param argument="--mode" type="select" label="Mode"> |
| 80 <option value="geno">Genome assemblies (DNA)</option> | 100 <option value="geno">Genome assemblies (DNA)</option> |
| 81 <option value="tran">Transcriptome assemblies (DNA)</option> | 101 <option value="tran">Transcriptome assemblies (DNA)</option> |
| 82 <option value="prot">annotated gene sets (protein)</option> | 102 <option value="prot">annotated gene sets (protein)</option> |
| 307 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" /> | 327 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" /> |
| 308 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" /> | 328 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" /> |
| 309 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" /> | 329 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" /> |
| 310 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" /> | 330 <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" /> |
| 311 </test> | 331 </test> |
| 332 <test expect_num_outputs="2"> | |
| 333 <param name="input" value="genome.fa" /> | |
| 334 <conditional name="lineage_conditional"> | |
| 335 <param name="selector" value="cached"/> | |
| 336 <param name="cached_db" value="busco-demo-db-20230328"/> | |
| 337 </conditional> | |
| 338 <conditional name="lineage"> | |
| 339 <param name="lineage_mode" value="select_lineage" /> | |
| 340 <param name="lineage_dataset" value="archaea_odb10" /> | |
| 341 </conditional> | |
| 342 <param name="outputs" value="short_summary" /> | |
| 343 <output name="busco_sum" file="genome_results/short_summary_cached" compare="diff" lines_diff="6" /> | |
| 344 <output name="busco_table" file="genome_results/full_table_cached" compare="diff" lines_diff="4" /> | |
| 345 <assert_stdout> | |
| 346 <has_text text="Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)"/> | |
| 347 </assert_stdout> | |
| 348 </test> | |
| 312 </tests> | 349 </tests> |
| 313 <help><![CDATA[ | 350 <help><![CDATA[ |
| 314 | 351 |
| 315 | 352 |
| 316 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs | 353 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs |