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comparison busco.xml @ 12:1278204240d8 draft

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"planemo upload commit d00431b92294849bd41d369d8a699e4669e5fc19"
author iuc
date Tue, 02 Nov 2021 09:40:29 +0000
parents 0d243f458b53
children 46ae58b1d792
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11:0d243f458b53 12:1278204240d8
1 <tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>assess genome assembly and annotation completeness</description> 2 <description>assess genome assembly and annotation completeness</description>
3 <xrefs>
4 <xref type="bio.tools">busco</xref>
5 </xrefs>
3 <macros> 6 <macros>
4 <import>macros.xml</import> 7 <import>macros.xml</import>
5 </macros> 8 </macros>
6 <requirements> 9 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">busco</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
20 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' && 23 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' &&
21 #end if 24 #end if
22 25
23 busco 26 busco
24 --in '${input}' 27 --in '${input}'
25 --lineage_dataset '${lineage_dataset}'
26 --update-data 28 --update-data
27 --mode '${busco_mode.mode}' 29 --mode '${busco_mode.mode}'
28 --out busco_galaxy 30 --out busco_galaxy
29 --cpu \${GALAXY_SLOTS:-4} 31 --cpu \${GALAXY_SLOTS:-4}
30 --evalue ${adv.evalue} 32 --evalue ${adv.evalue}
31 --limit ${adv.limit} 33 --limit ${adv.limit}
32 34
33 #if $adv.auto_lineage: 35 #if $lineage.lineage_mode == "auto_detect":
34 $adv.auto_lineage 36 $lineage.auto_lineage
37 #else if $lineage.lineage_mode == "select_lineage":
38 --lineage_dataset '${lineage.lineage_dataset}'
35 #end if 39 #end if
36 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes': 40 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
37 41
38 ${busco_mode.use_augustus.long} 42 ${busco_mode.use_augustus.long}
39 --augustus 43 --augustus
94 </when> 98 </when>
95 <when value="tran" /> 99 <when value="tran" />
96 <when value="prot" /> 100 <when value="prot" />
97 </conditional> 101 </conditional>
98 102
99 <param argument="--lineage_dataset" type="select" label="Lineage"> 103 <conditional name="lineage">
100 <expand macro="lineages" /> 104 <param name="lineage_mode" type="select" label="Auto-detect or select lineage?" help="Let BUSCO decide the best lineage automatically, or select from known lineage">
101 </param> 105 <option value="auto_detect">Auto-detect</option>
106 <option value="select_lineage">Select lineage</option>
107 </param>
108 <when value="auto_detect">
109 <param name="auto_lineage" type="select" label="auto-lineage group" help="Taxonomic group to run with auto-lineage.">
110 <option value="--auto-lineage">All taxonomic groups (--auto-lineage)</option>
111 <option value="--auto-lineage-prok">Prokaryotes (--auto-lineage-prok)</option>
112 <option value="--auto-lineage-euk">Eukaryotes (--auto-lineage-euk)</option>
113 </param>
114 </when>
115 <when value="select_lineage">
116 <param argument="--lineage_dataset" type="select" label="Lineage">
117 <expand macro="lineages" />
118 </param>
119 </when>
120 </conditional>
102 121
103 <section name="adv" title="Advanced Options" expanded="False"> 122 <section name="adv" title="Advanced Options" expanded="False">
104 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." /> 123 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
105 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" /> 124 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
106 <param name="auto_lineage" type="select" optional="true" label="Run auto-lineage to find optimal lineage path">
107 <option value="--auto-lineage">Run auto-lineage to find optimum lineage path</option>
108 <option value="--auto-lineage-prok">Run auto-lineage just on non-eukaryote trees to find optimum lineage path</option>
109 <option value="--auto-lineage-euk">Run auto-placement just on eukaryote tree to find optimum lineage path</option>
110 </param>
111 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> 125 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
112 <option value="short_summary">short summary text</option> 126 <option value="short_summary">short summary text</option>
113 <option value="missing">list with missing IDs</option> 127 <option value="missing">list with missing IDs</option>
114 <option value="image">summary image</option> 128 <option value="image">summary image</option>
115 </param> 129 </param>
128 </data> 142 </data>
129 </outputs> 143 </outputs>
130 <tests> 144 <tests>
131 <test expect_num_outputs="3"> 145 <test expect_num_outputs="3">
132 <param name="input" value="genome.fa" /> 146 <param name="input" value="genome.fa" />
133 <param name="lineage_dataset" value="arthropoda_odb10" /> 147 <conditional name="lineage">
148 <param name="lineage_mode" value="select_lineage" />
149 <param name="lineage_dataset" value="arthropoda_odb10" />
150 </conditional>
134 <conditional name="busco_mode"> 151 <conditional name="busco_mode">
135 <param name="mode" value="geno" /> 152 <param name="mode" value="geno" />
136 <conditional name="use_augustus"> 153 <conditional name="use_augustus">
137 <param name="use_augustus_selector" value="yes" /> 154 <param name="use_augustus_selector" value="yes" />
138 </conditional> 155 </conditional>
148 </assert_contents> 165 </assert_contents>
149 </output> 166 </output>
150 </test> 167 </test>
151 <test expect_num_outputs="4"> 168 <test expect_num_outputs="4">
152 <param name="input" value="proteome.fa" /> 169 <param name="input" value="proteome.fa" />
153 <param name="lineage_dataset" value="arthropoda_odb10" /> 170 <conditional name="lineage">
171 <param name="lineage_mode" value="select_lineage" />
172 <param name="lineage_dataset" value="arthropoda_odb10" />
173 </conditional>
154 <conditional name="busco_mode"> 174 <conditional name="busco_mode">
155 <param name="mode" value="prot" /> 175 <param name="mode" value="prot" />
156 </conditional> 176 </conditional>
157 <section name="adv"> 177 <section name="adv">
158 <param name="outputs" value="short_summary,missing,image" /> 178 <param name="outputs" value="short_summary,missing,image" />
162 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" /> 182 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
163 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> 183 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
164 </test> 184 </test>
165 <test expect_num_outputs="4"> 185 <test expect_num_outputs="4">
166 <param name="input" value="transcriptome.fa" /> 186 <param name="input" value="transcriptome.fa" />
167 <param name="lineage_dataset" value="arthropoda_odb10" /> 187 <conditional name="lineage">
188 <param name="lineage_mode" value="select_lineage" />
189 <param name="lineage_dataset" value="arthropoda_odb10" />
190 </conditional>
168 <conditional name="busco_mode"> 191 <conditional name="busco_mode">
169 <param name="mode" value="tran" /> 192 <param name="mode" value="tran" />
170 </conditional> 193 </conditional>
171 <section name="adv"> 194 <section name="adv">
172 <param name="auto_lineage" value="--auto-lineage" />
173 <param name="outputs" value="short_summary,missing,image" /> 195 <param name="outputs" value="short_summary,missing,image" />
174 </section> 196 </section>
175 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4" /> 197 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
176 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4" /> 198 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
177 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4" /> 199 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
178 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> 200 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
179 </test> 201 </test>
180 <test expect_num_outputs="2"> 202 <test expect_num_outputs="2">
181 <param name="input" value="genome.fa" /> 203 <param name="input" value="genome.fa" />
182 <param name="lineage_dataset" value="arthropoda_odb10" /> 204 <conditional name="lineage">
205 <param name="lineage_mode" value="select_lineage" />
206 <param name="lineage_dataset" value="arthropoda_odb10" />
207 </conditional>
183 <conditional name="busco_mode"> 208 <conditional name="busco_mode">
184 <param name="mode" value="geno" /> 209 <param name="mode" value="geno" />
185 <conditional name="use_augustus"> 210 <conditional name="use_augustus">
186 <param name="use_augustus_selector" value="yes" /> 211 <param name="use_augustus_selector" value="yes" />
187 <conditional name="aug_prediction"> 212 <conditional name="aug_prediction">
196 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> 221 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
197 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 222 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
198 </test> 223 </test>
199 <test expect_num_outputs="3"> 224 <test expect_num_outputs="3">
200 <param name="input" value="genome.fa" /> 225 <param name="input" value="genome.fa" />
201 <param name="lineage_dataset" value="arthropoda_odb10" /> 226 <conditional name="lineage">
227 <param name="lineage_mode" value="select_lineage" />
228 <param name="lineage_dataset" value="arthropoda_odb10" />
229 </conditional>
202 <conditional name="busco_mode"> 230 <conditional name="busco_mode">
203 <param name="mode" value="geno" /> 231 <param name="mode" value="geno" />
204 <conditional name="use_augustus"> 232 <conditional name="use_augustus">
205 <param name="use_augustus_selector" value="yes" /> 233 <param name="use_augustus_selector" value="yes" />
206 <conditional name="aug_prediction"> 234 <conditional name="aug_prediction">
216 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 244 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
217 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" /> 245 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
218 </test> 246 </test>
219 <test expect_num_outputs="4"> 247 <test expect_num_outputs="4">
220 <param name="input" value="genome.fa" /> 248 <param name="input" value="genome.fa" />
221 <param name="lineage_dataset" value="arthropoda_odb10" /> 249 <conditional name="lineage">
250 <param name="lineage_mode" value="select_lineage" />
251 <param name="lineage_dataset" value="arthropoda_odb10" />
252 </conditional>
222 <conditional name="busco_mode"> 253 <conditional name="busco_mode">
223 <param name="mode" value="geno" /> 254 <param name="mode" value="geno" />
224 <conditional name="use_augustus"> 255 <conditional name="use_augustus">
225 <param name="use_augustus_selector" value="no" /> 256 <param name="use_augustus_selector" value="no" />
226 </conditional> 257 </conditional>
227 </conditional> 258 </conditional>
228 <section name="adv"> 259 <section name="adv">
229 <param name="outputs" value="short_summary,missing,image" /> 260 <param name="outputs" value="short_summary,missing,image" />
230 </section> 261 </section>
231 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="4" /> 262 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />
232 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="4" /> 263 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
233 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="4" /> 264 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
234 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" /> 265 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
266 </test>
267 <test expect_num_outputs="4">
268 <param name="input" value="genome.fa" />
269 <conditional name="lineage">
270 <param name="lineage_mode" value="auto_detect" />
271 <param name="auto_lineage" value="--auto-lineage" />
272 </conditional>
273 <conditional name="busco_mode">
274 <param name="mode" value="geno" />
275 <conditional name="use_augustus">
276 <param name="use_augustus_selector" value="no" />
277 </conditional>
278 </conditional>
279 <section name="adv">
280 <param name="outputs" value="short_summary,missing,image" />
281 </section>
282 <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="4" />
283 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="0" />
284 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="0" />
285 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
235 </test> 286 </test>
236 </tests> 287 </tests>
237 <help><![CDATA[ 288 <help><![CDATA[
238 289
239 290