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planemo upload commit f7f94fe1eccafe1e29657bbd79197b4b32e03ffe
author iuc
date Thu, 12 Jan 2023 13:28:43 +0000
parents 7672c2794d4a
children eba1f3c7cd64
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15:7672c2794d4a 16:d4fbde719b2a
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 <macros>
4 <import>macros.xml</import>
5 </macros>
3 <xrefs> 6 <xrefs>
4 <xref type="bio.tools">busco</xref> 7 <xref type="bio.tools">busco</xref>
5 </xrefs> 8 </xrefs>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">busco</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
11 <requirement type="package" version="1.34">tar</requirement> 11 <requirement type="package" version="1.34">tar</requirement>
12 <requirement type="package" version="1">fonts-conda-ecosystem</requirement> 12 <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
13 </requirements> 13 </requirements>
14 <version_command>busco --version</version_command> 14 <version_command>busco --version</version_command>
15 <command><![CDATA[ 15 <command><![CDATA[
16
17 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
18
16 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi && 19 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
17 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ && 20 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
18 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ && 21 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
19 22
20 #if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes' and $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history': 23 #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
21 ## Using an augustus model from history, we need to unzip it and let augustus find it 24 ## Using an augustus model from history, we need to unzip it and let augustus find it
22 mkdir -p 'augustus_dir/species/' && 25 mkdir -p 'augustus_dir/species/' &&
23 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' && 26 tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' &&
27 #end if
28
24 #end if 29 #end if
25 30
26 busco 31 busco
27 --in '${input}' 32 --in '${input}'
28 --update-data 33 --update-data
55 && 60 &&
56 ls -l busco_galaxy/run_*/ && 61 ls -l busco_galaxy/run_*/ &&
57 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ 62 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
58 && 63 &&
59 generate_plot.py -wd BUSCO_summaries -rt specific 64 generate_plot.py -wd BUSCO_summaries -rt specific
65 #end if
66
67 #if $outputs and 'gff' in $outputs:
68 &&
69 echo "\##gff-version 3" > busco_output.gff
70 &&
71 ## gff files can be absent
72 cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true
60 #end if 73 #end if
61 74
62 ]]> </command> 75 ]]> </command>
63 <inputs> 76 <inputs>
64 <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." /> 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." />
121 134
122 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated"> 135 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
123 <option value="short_summary" selected="true">short summary text</option> 136 <option value="short_summary" selected="true">short summary text</option>
124 <option value="missing">list with missing IDs</option> 137 <option value="missing">list with missing IDs</option>
125 <option value="image">summary image</option> 138 <option value="image">summary image</option>
139 <option value="gff">gff</option>
126 </param> 140 </param>
127 141
128 <section name="adv" title="Advanced Options" expanded="False"> 142 <section name="adv" title="Advanced Options" expanded="False">
129 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." /> 143 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
130 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" /> 144 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
139 <filter>outputs and 'missing' in outputs</filter> 153 <filter>outputs and 'missing' in outputs</filter>
140 </data> 154 </data>
141 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png"> 155 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
142 <filter>outputs and 'image' in outputs</filter> 156 <filter>outputs and 'image' in outputs</filter>
143 </data> 157 </data>
158 <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">
159 <filter>outputs and 'gff' in outputs</filter>
160 </data>
144 </outputs> 161 </outputs>
145 <tests> 162 <tests>
146 <test expect_num_outputs="3"> 163 <test expect_num_outputs="4">
147 <param name="input" value="genome.fa" /> 164 <param name="input" value="genome.fa" />
148 <conditional name="lineage"> 165 <conditional name="lineage">
149 <param name="lineage_mode" value="select_lineage" /> 166 <param name="lineage_mode" value="select_lineage" />
150 <param name="lineage_dataset" value="arthropoda_odb10" /> 167 <param name="lineage_dataset" value="arthropoda_odb10" />
151 </conditional> 168 </conditional>
153 <param name="mode" value="geno" /> 170 <param name="mode" value="geno" />
154 <conditional name="use_augustus"> 171 <conditional name="use_augustus">
155 <param name="use_augustus_selector" value="yes" /> 172 <param name="use_augustus_selector" value="yes" />
156 </conditional> 173 </conditional>
157 </conditional> 174 </conditional>
158 <param name="outputs" value="short_summary,missing" /> 175 <param name="outputs" value="short_summary,missing,gff" />
159 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> 176 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
160 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 177 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
178 <output name="busco_gff">
179 <assert_contents>
180 <has_n_lines n="1"/>
181 <has_text text="##gff-version 3" />
182 </assert_contents>
183 </output>
161 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"> 184 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
162 <assert_contents> 185 <assert_contents>
163 <has_text text="# BUSCO version is: @TOOL_VERSION@" /> 186 <has_text text="# BUSCO version is: @TOOL_VERSION@" />
164 </assert_contents> 187 </assert_contents>
165 </output> 188 </output>
166 </test> 189 </test>
167 <test expect_num_outputs="4"> 190 <test expect_num_outputs="5">
168 <param name="input" value="proteome.fa" /> 191 <param name="input" value="proteome.fa" />
169 <conditional name="lineage"> 192 <conditional name="lineage">
170 <param name="lineage_mode" value="select_lineage" /> 193 <param name="lineage_mode" value="select_lineage" />
171 <param name="lineage_dataset" value="arthropoda_odb10" /> 194 <param name="lineage_dataset" value="arthropoda_odb10" />
172 </conditional> 195 </conditional>
173 <conditional name="busco_mode"> 196 <conditional name="busco_mode">
174 <param name="mode" value="prot" /> 197 <param name="mode" value="prot" />
175 </conditional> 198 </conditional>
176 <param name="outputs" value="short_summary,missing,image" /> 199 <param name="outputs" value="short_summary,missing,image,gff" />
177 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" /> 200 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" />
178 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" /> 201 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
179 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" /> 202 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
180 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> 203 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
181 </test> 204 <output name="busco_gff">
182 <test expect_num_outputs="4"> 205 <assert_contents>
206 <has_n_lines n="1"/>
207 <has_text text="##gff-version 3" />
208 </assert_contents>
209 </output>
210 </test>
211 <test expect_num_outputs="5">
183 <param name="input" value="transcriptome.fa" /> 212 <param name="input" value="transcriptome.fa" />
184 <conditional name="lineage"> 213 <conditional name="lineage">
185 <param name="lineage_mode" value="select_lineage" /> 214 <param name="lineage_mode" value="select_lineage" />
186 <param name="lineage_dataset" value="arthropoda_odb10" /> 215 <param name="lineage_dataset" value="arthropoda_odb10" />
187 </conditional> 216 </conditional>
188 <conditional name="busco_mode"> 217 <conditional name="busco_mode">
189 <param name="mode" value="tran" /> 218 <param name="mode" value="tran" />
190 </conditional> 219 </conditional>
191 <param name="outputs" value="short_summary,missing,image" /> 220 <param name="outputs" value="short_summary,missing,image,gff" />
192 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" /> 221 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
193 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" /> 222 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
194 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" /> 223 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
195 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> 224 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
196 </test> 225 <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" />
197 <test expect_num_outputs="2"> 226 </test>
227 <test expect_num_outputs="3">
198 <param name="input" value="genome.fa" /> 228 <param name="input" value="genome.fa" />
199 <conditional name="lineage"> 229 <conditional name="lineage">
200 <param name="lineage_mode" value="select_lineage" /> 230 <param name="lineage_mode" value="select_lineage" />
201 <param name="lineage_dataset" value="arthropoda_odb10" /> 231 <param name="lineage_dataset" value="arthropoda_odb10" />
202 </conditional> 232 </conditional>
208 <param name="augustus_mode" value="builtin" /> 238 <param name="augustus_mode" value="builtin" />
209 <param name="augustus_species" value="human" /> 239 <param name="augustus_species" value="human" />
210 </conditional> 240 </conditional>
211 </conditional> 241 </conditional>
212 </conditional> 242 </conditional>
213 <param name="outputs" value="short_summary" /> 243 <param name="outputs" value="short_summary,gff" />
214 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> 244 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
215 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 245 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
246 <output name="busco_gff">
247 <assert_contents>
248 <has_n_lines n="1"/>
249 <has_text text="##gff-version 3" />
250 </assert_contents>
251 </output>
216 </test> 252 </test>
217 <test expect_num_outputs="3"> 253 <test expect_num_outputs="3">
218 <param name="input" value="genome.fa" /> 254 <param name="input" value="genome.fa" />
219 <conditional name="lineage"> 255 <conditional name="lineage">
220 <param name="lineage_mode" value="select_lineage" /> 256 <param name="lineage_mode" value="select_lineage" />
233 <param name="outputs" value="short_summary,missing" /> 269 <param name="outputs" value="short_summary,missing" />
234 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> 270 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
235 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 271 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
236 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" /> 272 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
237 </test> 273 </test>
238 <test expect_num_outputs="4"> 274 <test expect_num_outputs="5">
239 <param name="input" value="genome.fa" /> 275 <param name="input" value="genome.fa" />
240 <conditional name="lineage"> 276 <conditional name="lineage">
241 <param name="lineage_mode" value="select_lineage" /> 277 <param name="lineage_mode" value="select_lineage" />
242 <param name="lineage_dataset" value="arthropoda_odb10" /> 278 <param name="lineage_dataset" value="arthropoda_odb10" />
243 </conditional> 279 </conditional>
245 <param name="mode" value="geno" /> 281 <param name="mode" value="geno" />
246 <conditional name="use_augustus"> 282 <conditional name="use_augustus">
247 <param name="use_augustus_selector" value="no" /> 283 <param name="use_augustus_selector" value="no" />
248 </conditional> 284 </conditional>
249 </conditional> 285 </conditional>
250 <param name="outputs" value="short_summary,missing,image" /> 286 <param name="outputs" value="short_summary,missing,image,gff" />
251 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" /> 287 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />
252 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" /> 288 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
253 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" /> 289 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
254 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" /> 290 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
255 </test> 291 <output name="busco_gff" file="genome_results_metaeuk/out.gff" compare="diff" />
256 <test expect_num_outputs="4"> 292 </test>
293 <test expect_num_outputs="5">
257 <param name="input" value="genome.fa" /> 294 <param name="input" value="genome.fa" />
258 <conditional name="lineage"> 295 <conditional name="lineage">
259 <param name="lineage_mode" value="auto_detect" /> 296 <param name="lineage_mode" value="auto_detect" />
260 <param name="auto_lineage" value="--auto-lineage" /> 297 <param name="auto_lineage" value="--auto-lineage" />
261 </conditional> 298 </conditional>
263 <param name="mode" value="geno" /> 300 <param name="mode" value="geno" />
264 <conditional name="use_augustus"> 301 <conditional name="use_augustus">
265 <param name="use_augustus_selector" value="no" /> 302 <param name="use_augustus_selector" value="no" />
266 </conditional> 303 </conditional>
267 </conditional> 304 </conditional>
268 <param name="outputs" value="short_summary,missing,image" /> 305 <param name="outputs" value="short_summary,missing,image,gff" />
269 <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" /> 306 <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" />
270 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" /> 307 <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="2" />
271 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" /> 308 <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" />
272 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" /> 309 <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" />
273 </test> 311 </test>
274 </tests> 312 </tests>
275 <help><![CDATA[ 313 <help><![CDATA[
276 314
277 315