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comparison sistr_cmd.xml @ 4:17fcac7ddf54 draft

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"planemo upload commit 5d0cc76371b061089f1399d21aea86540cbcab4f"
author nml
date Thu, 06 Aug 2020 11:48:49 -0400
parents 5c8ff92e38a9
children 24a7a95867b0
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3:5c8ff92e38a9 4:17fcac7ddf54
1 <tool id="sistr_cmd" name="sistr_cmd" version="1.0.2"> 1 <tool id="sistr_cmd" name="sistr_cmd" version="@VERSION@">
2 <description> 2 <description>
3 Salmonella In Silico Typing Resource commandline tool for serovar prediction 3 Salmonella In Silico Typing Resource commandline tool for serovar prediction
4 </description> 4 </description>
5 <macros>
6 <token name="@VERSION@">1.1.1</token>
7 </macros>
5 <requirements> 8 <requirements>
6 <requirement type="package" version="1.0.2">sistr_cmd</requirement> 9 <requirement type="package" version="@VERSION@">sistr_cmd</requirement>
7 </requirements> 10 </requirements>
8 <stdio> 11 <stdio>
9 <exit_code range="1:" /> 12 <exit_code range="1:" />
10 </stdio> 13 </stdio>
11 <command><![CDATA[ 14 <command><![CDATA[
159 format="json" 162 format="json"
160 label="cgMLST allele match results" /> 163 label="cgMLST allele match results" />
161 </outputs> 164 </outputs>
162 <tests> 165 <tests>
163 <test> 166 <test>
164 <param name="input_fastas" value="AE014613-699860.fasta"/> 167 <param name="input_fastas" value="AE014613-699860.fasta" ftype="fasta"/>
165 <param name="output_format" value="tab"/> 168 <param name="output_format" value="tab"/>
166 <output 169 <output
167 name="cgmlst_profiles" 170 name="cgmlst_profiles"
168 value="cgmlst-profiles.csv" 171 value="cgmlst-profiles.csv"
169 ftype="csv" 172 ftype="csv"
170 lines_diff="2"> 173 compare="diff">
171 <assert_contents> 174 </output>
172 <has_text text=",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,3969539340,2545200385,225275747,2955003506,2353669245,2666669453,1672513023,3779563470,1301843222,2161147266,607954140,3680021500,2914087704,1062106200,3673111880,1314942441,1367997025,3293595301,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1528212814,2110459436,4160823845,1648892875,2084418558,1638162324,469721942,1317894045,1973458150,926214622,2197498164,398274060,,,,,,,,,,1154766063,278162969,490843778,3950769715,,,,,,4203409135,2061008354,,,,,,,1052128508,,,1510445340,,,4065472468,,,,,,1495737522,,,,,,,,3076491138,712233770,3105746335,625241463,3016847250,1928860657,2229984332,1341416065,2978539204,1175502179,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1328452594,2372254687,2640609716,3051501604,3258707132,,,,,,,,,,,,1007978530,,3646345463,1109678443,,,,,,,,,"/> 175 <output name="output_prediction_tab"
173 </assert_contents>
174 </output>
175 <output
176 name="output_prediction_tab"
177 value="sistr-results.tab"
178 ftype="tabular" 176 ftype="tabular"
179 lines_diff="2"> 177 value="sistr-results.tabular"
178 compare="sim_size">
180 <assert_contents> 179 <assert_contents>
181 <has_text text="AE014613-699860" /> 180 <has_text text="AE014613-699860" />
182 <has_text text="Typhi" /> 181 <has_text text="Typhi" />
183 <has_text text="enterica" /> 182 <has_text text="enterica" />
184 <has_text text="-:-:-" /> 183 <has_text_matching expression="FAIL\t-\t-:-:-\t-:-:-"/>
185 <has_n_columns n="21" /> 184 <has_text text="2014-LET-0419"/>
185 <has_n_columns n="22" />
186 </assert_contents> 186 </assert_contents>
187 </output> 187 </output>
188 <output 188 <output
189 name="alleles_output" 189 name="alleles_output"
190 value="alleles-output.json" 190 value="alleles-output.json"
191 ftype="json" 191 ftype="json"
192 compare="sim_size"/> 192 compare="sim_size">
193 <assert_contents>
194 <has_text text="NZ_AOXE01000059.1"/>
195 <has_text text="Salmonella enterica subsp. enterica serovar Typhi Ty2"/>
196 <has_text text="NZ_AOXE01000033.1"/>
197 <has_text text="NZ_AOXE01000052.1"/>
198 </assert_contents>
199 </output>
193 </test> 200 </test>
194 <test> 201 <test>
195 <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/> 202 <param name="input_fastas" value="13-1101-Paratyphi_B.fasta" ftype="fasta"/>
196 <param name="output_format" value="tab"/> 203 <param name="output_format" value="tab"/>
197 <output 204 <output
198 name="novel_alleles" 205 name="novel_alleles"
199 value="novel-alleles-13-1101.fasta" 206 value="novel-alleles-13-1101.fasta"
200 ftype="fasta" 207 ftype="fasta"
201 compare="sim_size"/> 208 compare="sim_size"/>
202 <output 209 <output
203 name="cgmlst_profiles" 210 name="cgmlst_profiles"
204 value="cgmlst-profiles-13-1101.csv" 211 value="cgmlst-profiles-13-1101.csv"
205 ftype="csv" 212 ftype="csv"
206 lines_diff="2"> 213 compare="diff">
207 </output> 214 </output>
208 <output 215 <output
209 name="output_prediction_tab" 216 name="output_prediction_tab"
210 value="sistr-results-13-1101.tab" 217 value="sistr-results-13-1101.tabular"
211 ftype="tabular" 218 ftype="tabular"
212 lines_diff="2"> 219 compare="sim_size">
213 <assert_contents> 220 <assert_contents>
214 <has_text text="13-1101-Paratyphi_B" /> 221 <has_text text="13-1101-Paratyphi_B"/>
215 <has_text text="Paratyphi B var. Java" /> 222 <has_text text="Paratyphi B var. Java"/>
216 <has_text text="enterica" /> 223 <has_text text="enterica"/>
217 <has_text text="1,4,[5],12" /> 224 <has_text text="1,4,[5],12"/>
218 <has_text text="PASS" /> 225 <has_text text="PASS"/>
219 <has_n_columns n="21" /> 226 <has_n_columns n="22"/>
220 </assert_contents> 227 </assert_contents>
221 </output> 228 </output>
222 <output 229 <output
223 name="alleles_output" 230 name="alleles_output"
224 value="alleles-output-13-1101.json" 231 value="alleles-output-13-1101.json"
225 ftype="json" 232 ftype="json"
226 compare="sim_size"/>
227 </test>
228 <test>
229 <param name="input_fastas" value="13-1101 Paratyphi_B.fasta"/>
230 <param name="output_format" value="tab"/>
231 <output
232 name="novel_alleles"
233 value="novel-alleles-13-1101.fasta"
234 ftype="fasta"
235 compare="sim_size"/>
236 <output
237 name="cgmlst_profiles"
238 value="cgmlst-profiles-13-1101.csv"
239 ftype="csv"
240 lines_diff="2">
241 </output>
242 <output
243 name="output_prediction_tab"
244 value="sistr-results-13-1101.tab"
245 ftype="tabular"
246 lines_diff="2">
247 <assert_contents>
248 <has_text text="13-1101 Paratyphi_B" />
249 <has_text text="Paratyphi B var. Java" />
250 <has_text text="enterica" />
251 <has_text text="1,4,[5],12" />
252 <has_text text="PASS" />
253 <has_n_columns n="21" />
254 </assert_contents>
255 </output>
256 <output
257 name="alleles_output"
258 value="alleles-output-13-1101.json"
259 ftype="json"
260 compare="sim_size"/>
261 </test>
262 <test>
263 <param name="input_fastas" value="13-1101-Paratyphi_B.fasta"/>
264 <param name="output_format" value="json"/>
265 <param name="more_output" value="-MM"/>
266 <output
267 name="output_prediction_json"
268 value="sistr-results-13-1101.json"
269 ftype="json"
270 compare="sim_size"> 233 compare="sim_size">
271 <assert_contents> 234 <assert_contents>
272 <has_text text="13-1101-Paratyphi_B" /> 235 <has_text text="13-1101-Paratyphi_B"/>
273 <has_text text="Paratyphi B var. Java" /> 236 <has_text text="NZ_AOXE01000059.1"/>
274 <has_text text="enterica" />
275 <has_text text="1,4,[5],12" />
276 <has_text text="PASS" />
277 </assert_contents> 237 </assert_contents>
278 </output> 238 </output>
279 </test> 239 </test>
280 </tests> 240 </tests>
281 <help> 241 <help>
282 <![CDATA[ 242 <![CDATA[
283 243