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comparison busco.xml @ 18:94170eee0ad8 draft

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planemo upload commit 09dff03131fb917a00cc291580ed7c4f38b266c9
author iuc
date Fri, 14 Apr 2023 08:13:46 +0000
parents e824f5d958d0
children 2a5b8b9936bf
comparison
equal deleted inserted replaced
17:e824f5d958d0 18:94170eee0ad8
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