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comparison busco.xml @ 19:2a5b8b9936bf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit a01d758e10182682225b368696791dd39d6cc820
author iuc
date Tue, 14 Nov 2023 13:03:37 +0000
parents 94170eee0ad8
children ea8146ee148f
comparison
equal deleted inserted replaced
18:94170eee0ad8 19:2a5b8b9936bf
33 --mode '${busco_mode.mode}' 33 --mode '${busco_mode.mode}'
34 --out busco_galaxy 34 --out busco_galaxy
35 --cpu \${GALAXY_SLOTS:-4} 35 --cpu \${GALAXY_SLOTS:-4}
36 --evalue ${adv.evalue} 36 --evalue ${adv.evalue}
37 --limit ${adv.limit} 37 --limit ${adv.limit}
38 --contig_break ${adv.contig_break}
38 39
39 #if $lineage_conditional.selector == 'cached': 40 #if $lineage_conditional.selector == 'cached':
40 --offline 41 --offline
41 --download_path $lineage_conditional.cached_db.fields.path 42 --download_path $lineage_conditional.cached_db.fields.path
42 #else 43 #else
46 #if $lineage.lineage_mode == "auto_detect": 47 #if $lineage.lineage_mode == "auto_detect":
47 $lineage.auto_lineage 48 $lineage.auto_lineage
48 #else if $lineage.lineage_mode == "select_lineage": 49 #else if $lineage.lineage_mode == "select_lineage":
49 --lineage_dataset '${lineage.lineage_dataset}' 50 --lineage_dataset '${lineage.lineage_dataset}'
50 #end if 51 #end if
52
51 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes': 53 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
52 54
53 ${busco_mode.use_augustus.long} 55 ${busco_mode.use_augustus.long}
54 --augustus 56 --augustus
55 57
58 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history': 60 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
59 --augustus_species local 61 --augustus_species local
60 #end if 62 #end if
61 #end if 63 #end if
62 64
65 #if str( $busco_mode.mode ) == "geno":
66 #if $busco_mode.miniprot:
67 --miniprot
68 #end if
69 #end if
70
63 #if $outputs and 'image' in $outputs: 71 #if $outputs and 'image' in $outputs:
64 && 72 &&
65 mkdir BUSCO_summaries 73 mkdir BUSCO_summaries
66 && 74 &&
67 ls -l busco_galaxy/run_*/ && 75 ls -l busco_galaxy/run_*/ &&
75 echo "\##gff-version 3" > busco_output.gff 83 echo "\##gff-version 3" > busco_output.gff
76 && 84 &&
77 ## gff files can be absent 85 ## gff files can be absent
78 cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true 86 cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
79 #end if 87 #end if
88
80 89
81 ]]> </command> 90 ]]> </command>
82 <inputs> 91 <inputs>
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." /> 92 <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"> 93 <conditional name="lineage_conditional">
100 <option value="geno">Genome assemblies (DNA)</option> 109 <option value="geno">Genome assemblies (DNA)</option>
101 <option value="tran">Transcriptome assemblies (DNA)</option> 110 <option value="tran">Transcriptome assemblies (DNA)</option>
102 <option value="prot">annotated gene sets (protein)</option> 111 <option value="prot">annotated gene sets (protein)</option>
103 </param> 112 </param>
104 <when value="geno"> 113 <when value="geno">
114 <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/>
105 <conditional name="use_augustus"> 115 <conditional name="use_augustus">
106 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk"> 116 <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
107 <option value="yes">Yes, use Augustus</option> 117 <option value="yes">Yes, use Augustus</option>
108 <option value="no" selected="true">Use Metaeuk</option> 118 <option value="no" selected="true">Use Metaeuk</option>
109 </param> 119 </param>
160 </param> 170 </param>
161 171
162 <section name="adv" title="Advanced Options" expanded="False"> 172 <section name="adv" title="Advanced Options" expanded="False">
163 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." /> 173 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
164 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" /> 174 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
175 <param argument="--contig_break" type="integer" value="10" label="Number of contiguous Ns to signify a break between contigs"/>
165 </section> 176 </section>
166 </inputs> 177 </inputs>
178
167 <outputs> 179 <outputs>
168 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"> 180 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
169 <filter>outputs and 'short_summary' in outputs</filter> 181 <filter>outputs and 'short_summary' in outputs</filter>
170 </data> 182 </data>
171 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" /> 183 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
176 <filter>outputs and 'image' in outputs</filter> 188 <filter>outputs and 'image' in outputs</filter>
177 </data> 189 </data>
178 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff"> 190 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
179 <filter>outputs and 'gff' in outputs</filter> 191 <filter>outputs and 'gff' in outputs</filter>
180 </data> 192 </data>
193 <data name='busco_miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff">
194 <filter>busco_mode['mode'] == 'geno' and busco_mode['miniprot']</filter>
195 </data>
181 </outputs> 196 </outputs>
197
182 <tests> 198 <tests>
183 <test expect_num_outputs="4"> 199 <test expect_num_outputs="4">
184 <param name="input" value="genome.fa" /> 200 <param name="input" value="genome.fa" />
185 <conditional name="lineage"> 201 <conditional name="lineage">
186 <param name="lineage_mode" value="select_lineage" /> 202 <param name="lineage_mode" value="select_lineage" />
242 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" /> 258 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
243 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" /> 259 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
244 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> 260 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
245 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" /> 261 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
246 </test> 262 </test>
247 <test expect_num_outputs="3"> 263 <test expect_num_outputs="4">
248 <param name="input" value="genome.fa" /> 264 <param name="input" value="genome.fa" />
249 <conditional name="lineage"> 265 <conditional name="lineage">
250 <param name="lineage_mode" value="select_lineage" /> 266 <param name="lineage_mode" value="select_lineage" />
251 <param name="lineage_dataset" value="arthropoda_odb10" /> 267 <param name="lineage_dataset" value="arthropoda_odb10" />
252 </conditional> 268 </conditional>
253 <conditional name="busco_mode"> 269 <conditional name="busco_mode">
254 <param name="mode" value="geno" /> 270 <param name="mode" value="geno" />
271 <param name="miniprot" value="true"/>
255 <conditional name="use_augustus"> 272 <conditional name="use_augustus">
256 <param name="use_augustus_selector" value="yes" /> 273 <param name="use_augustus_selector" value="yes" />
257 <conditional name="aug_prediction"> 274 <conditional name="aug_prediction">
258 <param name="augustus_mode" value="builtin" /> 275 <param name="augustus_mode" value="builtin" />
259 <param name="augustus_species" value="human" /> 276 <param name="augustus_species" value="human" />
267 <assert_contents> 284 <assert_contents>
268 <has_n_lines n="1"/> 285 <has_n_lines n="1"/>
269 <has_text text="##gff-version 3" /> 286 <has_text text="##gff-version 3" />
270 </assert_contents> 287 </assert_contents>
271 </output> 288 </output>
289 <!-- The miniprot.gff file is too large. A file containing only the first 1000 lines is used for this test. -->
290 <output name="busco_miniprot" file="genome_results/miniprot_1000.gff" compare="contains" lines_diff="304463"/>
272 </test> 291 </test>
273 <test expect_num_outputs="3"> 292 <test expect_num_outputs="3">
274 <param name="input" value="genome.fa" /> 293 <param name="input" value="genome.fa" />
275 <conditional name="lineage"> 294 <conditional name="lineage">
276 <param name="lineage_mode" value="select_lineage" /> 295 <param name="lineage_mode" value="select_lineage" />