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comparison busco.xml @ 13:46ae58b1d792 draft

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"planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
author iuc
date Fri, 05 Nov 2021 08:41:35 +0000
parents 1278204240d8
children 41030a6c03b7
comparison
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12:1278204240d8 13:46ae58b1d792
47 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history': 47 #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
48 --augustus_species local 48 --augustus_species local
49 #end if 49 #end if
50 #end if 50 #end if
51 51
52 #if $adv.outputs and 'image' in $adv.outputs: 52 #if $outputs and 'image' in $outputs:
53 && 53 &&
54 mkdir BUSCO_summaries 54 mkdir BUSCO_summaries
55 && 55 &&
56 ls -l busco_galaxy/run_*/ && 56 ls -l busco_galaxy/run_*/ &&
57 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ 57 cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
117 <expand macro="lineages" /> 117 <expand macro="lineages" />
118 </param> 118 </param>
119 </when> 119 </when>
120 </conditional> 120 </conditional>
121 121
122 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
123 <option value="short_summary" selected="true">short summary text</option>
124 <option value="missing">list with missing IDs</option>
125 <option value="image">summary image</option>
126 </param>
127
122 <section name="adv" title="Advanced Options" expanded="False"> 128 <section name="adv" title="Advanced Options" expanded="False">
123 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." /> 129 <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
124 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" /> 130 <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
125 <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
126 <option value="short_summary">short summary text</option>
127 <option value="missing">list with missing IDs</option>
128 <option value="image">summary image</option>
129 </param>
130 </section> 131 </section>
131 </inputs> 132 </inputs>
132 <outputs> 133 <outputs>
133 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"> 134 <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
134 <filter>adv['outputs'] and 'short_summary' in adv['outputs']</filter> 135 <filter>outputs and 'short_summary' in outputs</filter>
135 </data> 136 </data>
136 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" /> 137 <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
137 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv"> 138 <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
138 <filter>adv['outputs'] and 'missing' in adv['outputs']</filter> 139 <filter>outputs and 'missing' in outputs</filter>
139 </data> 140 </data>
140 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png"> 141 <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
141 <filter>adv['outputs'] and 'image' in adv['outputs']</filter> 142 <filter>outputs and 'image' in outputs</filter>
142 </data> 143 </data>
143 </outputs> 144 </outputs>
144 <tests> 145 <tests>
145 <test expect_num_outputs="3"> 146 <test expect_num_outputs="3">
146 <param name="input" value="genome.fa" /> 147 <param name="input" value="genome.fa" />
152 <param name="mode" value="geno" /> 153 <param name="mode" value="geno" />
153 <conditional name="use_augustus"> 154 <conditional name="use_augustus">
154 <param name="use_augustus_selector" value="yes" /> 155 <param name="use_augustus_selector" value="yes" />
155 </conditional> 156 </conditional>
156 </conditional> 157 </conditional>
157 <section name="adv"> 158 <param name="outputs" value="short_summary,missing" />
158 <param name="outputs" value="short_summary,missing" />
159 </section>
160 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> 159 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
161 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 160 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
162 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"> 161 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
163 <assert_contents> 162 <assert_contents>
164 <has_text text="# BUSCO version is: @TOOL_VERSION@" /> 163 <has_text text="# BUSCO version is: @TOOL_VERSION@" />
172 <param name="lineage_dataset" value="arthropoda_odb10" /> 171 <param name="lineage_dataset" value="arthropoda_odb10" />
173 </conditional> 172 </conditional>
174 <conditional name="busco_mode"> 173 <conditional name="busco_mode">
175 <param name="mode" value="prot" /> 174 <param name="mode" value="prot" />
176 </conditional> 175 </conditional>
177 <section name="adv"> 176 <param name="outputs" value="short_summary,missing,image" />
178 <param name="outputs" value="short_summary,missing,image" />
179 </section>
180 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" /> 177 <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" />
181 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" /> 178 <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
182 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" /> 179 <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
183 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> 180 <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
184 </test> 181 </test>
189 <param name="lineage_dataset" value="arthropoda_odb10" /> 186 <param name="lineage_dataset" value="arthropoda_odb10" />
190 </conditional> 187 </conditional>
191 <conditional name="busco_mode"> 188 <conditional name="busco_mode">
192 <param name="mode" value="tran" /> 189 <param name="mode" value="tran" />
193 </conditional> 190 </conditional>
194 <section name="adv"> 191 <param name="outputs" value="short_summary,missing,image" />
195 <param name="outputs" value="short_summary,missing,image" />
196 </section>
197 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" /> 192 <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="6" />
198 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" /> 193 <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" />
199 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" /> 194 <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" />
200 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> 195 <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
201 </test> 196 </test>
213 <param name="augustus_mode" value="builtin" /> 208 <param name="augustus_mode" value="builtin" />
214 <param name="augustus_species" value="human" /> 209 <param name="augustus_species" value="human" />
215 </conditional> 210 </conditional>
216 </conditional> 211 </conditional>
217 </conditional> 212 </conditional>
218 <section name="adv"> 213 <param name="outputs" value="short_summary" />
219 <param name="outputs" value="short_summary" />
220 </section>
221 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> 214 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
222 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 215 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
223 </test> 216 </test>
224 <test expect_num_outputs="3"> 217 <test expect_num_outputs="3">
225 <param name="input" value="genome.fa" /> 218 <param name="input" value="genome.fa" />
235 <param name="augustus_mode" value="history" /> 228 <param name="augustus_mode" value="history" />
236 <param name="augustus_model" value="local.tar.gz" ftype="augustus" /> 229 <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
237 </conditional> 230 </conditional>
238 </conditional> 231 </conditional>
239 </conditional> 232 </conditional>
240 <section name="adv"> 233 <param name="outputs" value="short_summary,missing" />
241 <param name="outputs" value="short_summary,missing" />
242 </section>
243 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" /> 234 <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
244 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> 235 <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
245 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" /> 236 <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
246 </test> 237 </test>
247 <test expect_num_outputs="4"> 238 <test expect_num_outputs="4">
254 <param name="mode" value="geno" /> 245 <param name="mode" value="geno" />
255 <conditional name="use_augustus"> 246 <conditional name="use_augustus">
256 <param name="use_augustus_selector" value="no" /> 247 <param name="use_augustus_selector" value="no" />
257 </conditional> 248 </conditional>
258 </conditional> 249 </conditional>
259 <section name="adv"> 250 <param name="outputs" value="short_summary,missing,image" />
260 <param name="outputs" value="short_summary,missing,image" />
261 </section>
262 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" /> 251 <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="6" />
263 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" /> 252 <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" />
264 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" /> 253 <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" />
265 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" /> 254 <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
266 </test> 255 </test>
274 <param name="mode" value="geno" /> 263 <param name="mode" value="geno" />
275 <conditional name="use_augustus"> 264 <conditional name="use_augustus">
276 <param name="use_augustus_selector" value="no" /> 265 <param name="use_augustus_selector" value="no" />
277 </conditional> 266 </conditional>
278 </conditional> 267 </conditional>
279 <section name="adv"> 268 <param name="outputs" value="short_summary,missing,image" />
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" /> 269 <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" /> 270 <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" /> 271 <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" /> 272 <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />
286 </test> 273 </test>