Mercurial > repos > iuc > busco
comparison busco.xml @ 13:46ae58b1d792 draft
"planemo upload commit 2adcb199f279b9ea1c3896a1f7a5b8cd9311228b"
| author | iuc |
|---|---|
| date | Fri, 05 Nov 2021 08:41:35 +0000 |
| parents | 1278204240d8 |
| children | 41030a6c03b7 |
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| 12:1278204240d8 | 13:46ae58b1d792 |
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| 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> |