Mercurial > repos > greg > vsnp_get_snps

comparison vsnp_get_snps.xml @ 14:44b84d32883c draft default tip

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"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit 7f5ebaad2e650c53a8980e8567fe9943f9ccabb6"
author greg
date Mon, 15 Nov 2021 23:14:34 +0000
parents cd636b0e4f95
children
comparison
equal deleted inserted replaced
13:cd636b0e4f95 14:44b84d32883c
129 </when> 129 </when>
130 </conditional> 130 </conditional>
131 </when> 131 </when>
132 <when value="no"/> 132 <when value="no"/>
133 </conditional> 133 </conditional>
134 <param argument="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="true" label="Create a group containing all isolates?"/> 134 <param name="all_isolates" type="boolean" truevalue="--all_isolates" falsevalue="" checked="true" label="Create a group containing all isolates?"/>
135 </inputs> 135 </inputs>
136 <outputs> 136 <outputs>
137 <collection name="snps" type="list" label="${tool.name} on ${on_string} (SNPs)"> 137 <collection name="snps" type="list" label="${tool.name} on ${on_string} (SNPs)">
138 <discover_datasets pattern="__name_and_ext__" directory="output_snps_dir"/> 138 <discover_datasets pattern="__name_and_ext__" directory="output_snps_dir"/>
139 </collection> 139 </collection>
164 </collection> 164 </collection>
165 </param> 165 </param>
166 <param name="input_excel_param" value="no"/> 166 <param name="input_excel_param" value="no"/>
167 <param name="all_isolates" value=""/> 167 <param name="all_isolates" value=""/>
168 <output_collection name="snps" type="list" count="1"> 168 <output_collection name="snps" type="list" count="1">
169 <element name="all_vcf" file="all_vcf.fasta" ftype="fasta" compare="contains"/> 169 <element name="all_vcf" ftype="fasta">
170 <assert_contents>
171 <has_size value="150"/>
172 </assert_contents>
173 </element>
170 </output_collection> 174 </output_collection>
171 <output_collection name="json_avg_mq" type="list" count="1"> 175 <output_collection name="json_avg_mq" type="list" count="1">
172 <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/> 176 <element name="all_vcf" ftype="json">
177 <assert_contents>
178 <has_size value="551"/>
179 </assert_contents>
180 </element>
173 </output_collection> 181 </output_collection>
174 <output_collection name="json_snps" type="list" count="1"> 182 <output_collection name="json_snps" type="list" count="1">
175 <element name="all_vcf" file="json_all_vcf.json" ftype="json" compare="contains"/> 183 <element name="all_vcf" ftype="json">
176 </output_collection> 184 <assert_contents>
177 <output name="output_summary" file="output_summary.html" ftype="html" compare="contains"/> 185 <has_size value="876"/>
186 </assert_contents>
187 </element>
188 </output_collection>
189 <output name="output_summary" ftype="html">
190 <assert_contents>
191 <has_size value="303"/>
192 </assert_contents>
193 </output>
178 </test> 194 </test>
179 <!-- An input collection, no excel file, all_isolates is False --> 195 <!-- An input collection, no excel file, all_isolates is False -->
180 <test expect_num_outputs="4"> 196 <test expect_num_outputs="4">
181 <param name="input_zc_vcf_type" value="collection"/> 197 <param name="input_zc_vcf_type" value="collection"/>
182 <param name="input_zc_vcf_collection"> 198 <param name="input_zc_vcf_collection">
194 </collection> 210 </collection>
195 </param> 211 </param>
196 <param name="input_excel_param" value="no"/> 212 <param name="input_excel_param" value="no"/>
197 <param name="all_isolates" value=""/> 213 <param name="all_isolates" value=""/>
198 <output_collection name="snps" type="list" count="1"> 214 <output_collection name="snps" type="list" count="1">
199 <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/> 215 <element name="all_vcf" ftype="fasta">
216 <assert_contents>
217 <has_size value="5226"/>
218 </assert_contents>
219 </element>
200 </output_collection> 220 </output_collection>
201 <output_collection name="json_avg_mq" type="list" count="1"> 221 <output_collection name="json_avg_mq" type="list" count="1">
202 <element name="all_vcf" file="json_avg_mq_all_vcf.json" ftype="json" compare="contains"/> 222 <element name="all_vcf" ftype="json">
223 <assert_contents>
224 <has_size value="24332"/>
225 </assert_contents>
226 </element>
203 </output_collection> 227 </output_collection>
204 <output_collection name="json_snps" type="list" count="1"> 228 <output_collection name="json_snps" type="list" count="1">
205 <element name="all_vcf" file="json_all_vcf.json" ftype="json" compare="contains"/> 229 <element name="all_vcf" ftype="json">
206 </output_collection> 230 <assert_contents>
207 <output name="output_summary" file="output_summary2.html" ftype="html" compare="contains"/> 231 <has_size value="38798"/>
232 </assert_contents>
233 </element>
234 </output_collection>
235 <output name="output_summary" ftype="html">
236 <assert_contents>
237 <has_size value="303"/>
238 </assert_contents>
239 </output>
208 </test> 240 </test>
209 <!-- An input collection, an excel file, all_isolates is False --> 241 <!-- An input collection, an excel file, all_isolates is False -->
210 <test expect_num_outputs="4"> 242 <test expect_num_outputs="4">
211 <param name="input_zc_vcf_type" value="collection"/> 243 <param name="input_zc_vcf_type" value="collection"/>
212 <param name="input_zc_vcf_collection"> 244 <param name="input_zc_vcf_collection">
225 </param> 257 </param>
226 <param name="input_excel_param" value="yes"/> 258 <param name="input_excel_param" value="yes"/>
227 <param name="input_excel" value="89"/> 259 <param name="input_excel" value="89"/>
228 <param name="all_isolates" value=""/> 260 <param name="all_isolates" value=""/>
229 <output_collection name="snps" type="list" count="1"> 261 <output_collection name="snps" type="list" count="1">
230 <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta" compare="contains"/> 262 <element name="Mbovis-17" ftype="fasta">
263 <assert_contents>
264 <has_size value="749"/>
265 </assert_contents>
266 </element>
231 </output_collection> 267 </output_collection>
232 <output_collection name="json_avg_mq" type="list" count="1"> 268 <output_collection name="json_avg_mq" type="list" count="1">
233 <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> 269 <element name="Mbovis-17" ftype="json">
270 <assert_contents>
271 <has_size value="10884"/>
272 </assert_contents>
273 </element>
234 </output_collection> 274 </output_collection>
235 <output_collection name="json_snps" type="list" count="1"> 275 <output_collection name="json_snps" type="list" count="1">
236 <element name="Mbovis-17" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/> 276 <element name="Mbovis-17" ftype="json">
237 </output_collection> 277 <assert_contents>
238 <output name="output_summary" file="output_summary3.html" ftype="html" compare="contains"/> 278 <has_size value="6396"/>
279 </assert_contents>
280 </element>
281 </output_collection>
282 <output name="output_summary" ftype="html">
283 <assert_contents>
284 <has_size value="1057"/>
285 </assert_contents>
286 </output>
239 </test> 287 </test>
240 <!-- An input collection, an excel file, all_isolates is True --> 288 <!-- An input collection, an excel file, all_isolates is True -->
241 <test expect_num_outputs="4"> 289 <test expect_num_outputs="4">
242 <param name="input_zc_vcf_type" value="collection"/> 290 <param name="input_zc_vcf_type" value="collection"/>
243 <param name="input_zc_vcf_collection"> 291 <param name="input_zc_vcf_collection">
256 </param> 304 </param>
257 <param name="input_excel_param" value="yes"/> 305 <param name="input_excel_param" value="yes"/>
258 <param name="input_excel" value="89"/> 306 <param name="input_excel" value="89"/>
259 <param name="all_isolates" value="--all_isolates"/> 307 <param name="all_isolates" value="--all_isolates"/>
260 <output_collection name="snps" type="list" count="2"> 308 <output_collection name="snps" type="list" count="2">
261 <element name="Mbovis-17" file="Mbovis-17_snps.fasta" ftype="fasta" compare="contains"/> 309 <element name="Mbovis-17" ftype="fasta">
262 <element name="all_vcf" file="all_vcf2.fasta" ftype="fasta" compare="contains"/> 310 <assert_contents>
311 <has_size value="749"/>
312 </assert_contents>
313 </element>
314 <element name="all_vcf" ftype="fasta">
315 <assert_contents>
316 <has_size value="4920"/>
317 </assert_contents>
318 </element>
263 </output_collection> 319 </output_collection>
264 <output_collection name="json_avg_mq" type="list" count="2"> 320 <output_collection name="json_avg_mq" type="list" count="2">
265 <element name="Mbovis-17" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> 321 <element name="Mbovis-17" ftype="json">
266 <element name="all_vcf" file="Mbovis-17_avg_mq_json.json" ftype="json" compare="contains"/> 322 <assert_contents>
323 <has_size value="10884"/>
324 </assert_contents>
325 </element>
326 <element name="all_vcf" ftype="json">
327 <assert_contents>
328 <has_size value="24332"/>
329 </assert_contents>
330 </element>
267 </output_collection> 331 </output_collection>
268 <output_collection name="json_snps" type="list" count="2"> 332 <output_collection name="json_snps" type="list" count="2">
269 <element name="Mbovis-17" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/> 333 <element name="Mbovis-17" ftype="json">
270 <element name="all_vcf" file="Mbovis-17_snps_json.json" ftype="json" compare="contains"/> 334 <assert_contents>
271 </output_collection> 335 <has_size value="6396"/>
272 <output name="output_summary" file="output_summary4.html" ftype="html" compare="contains"/> 336 </assert_contents>
337 </element>
338 <element name="all_vcf" ftype="json">
339 <assert_contents>
340 <has_size value="36466"/>
341 </assert_contents>
342 </element>
343 </output_collection>
344 <output name="output_summary" ftype="html">
345 <assert_contents>
346 <has_size value="1056"/>
347 </assert_contents>
348 </output>
273 </test> 349 </test>
274 </tests> 350 </tests>
275 <help> 351 <help>
276 **What it does** 352 **What it does**
277 353