Mercurial > repos > iuc > data_manager_mothur_toolsuite
comparison data_manager/data_manager_fetch_mothur_reference_data.xml @ 2:0e532fc0a0a6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309"
author | iuc |
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date | Thu, 17 Sep 2020 09:37:41 +0000 |
parents | aec831b54a5b |
children | 0db22932bc39 |
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1:aec831b54a5b | 2:0e532fc0a0a6 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.4" tool_type="manage_data" profile="19.05"> | 2 <tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.5" tool_type="manage_data" profile="19.05"> |
3 <description>Fetch and install reference data for Mothur</description> | 3 <description>Fetch and install reference data for Mothur</description> |
4 <requirements> | 4 <requirements> |
5 <requirement type="package" version="2.7">python</requirement> | 5 <requirement type="package" version="2.7">python</requirement> |
6 </requirements> | 6 </requirements> |
7 <command><![CDATA[ | 7 <command><![CDATA[ |
72 <has_text text="GS FLX Titanium" /> | 72 <has_text text="GS FLX Titanium" /> |
73 <has_text text="LookUp_Titanium.pat" /> | 73 <has_text text="LookUp_Titanium.pat" /> |
74 </assert_contents> | 74 </assert_contents> |
75 </output> | 75 </output> |
76 </test> | 76 </test> |
77 <test> | |
78 <param name="data_source|ref_data" value="lookup_gsflx"/> | |
79 <output name="out_file"> | |
80 <assert_contents> | |
81 <has_text text="GSFLX" /> | |
82 <has_text text="LookUp_GSFLX.pat" /> | |
83 </assert_contents> | |
84 </output> | |
85 </test> | |
86 <test> | |
87 <param name="data_source|ref_data" value="lookup_gs20"/> | |
88 <output name="out_file"> | |
89 <assert_contents> | |
90 <has_text text="GS20" /> | |
91 <has_text text="LookUp_GS20.pat" /> | |
92 </assert_contents> | |
93 </output> | |
94 </test> | |
95 <test> | |
96 <param name="data_source|ref_data" value="RDP_v16"/> | |
97 <output name="out_file"> | |
98 <assert_contents> | |
99 <has_text text="16S rRNA RDP training set 16" /> | |
100 <has_text text="trainset16_022016.rdp.fasta" /> | |
101 <has_text text="trainset16_022016.rdp.tax" /> | |
102 <has_text text="trainset16_022016.pds.fasta" /> | |
103 <has_text text="trainset16_022016.pds.tax" /> | |
104 </assert_contents> | |
105 </output> | |
106 </test> | |
107 <test> | |
108 <param name="data_source|ref_data" value="RDP_v14"/> | |
109 <output name="out_file"> | |
110 <assert_contents> | |
111 <has_text text="16S rRNA RDP training set 14" /> | |
112 <has_text text="trainset14_032015.rdp.fasta" /> | |
113 <has_text text="trainset14_032015.rdp.tax" /> | |
114 <has_text text="trainset14_032015.pds.fasta" /> | |
115 <has_text text="trainset14_032015.pds.tax" /> | |
116 </assert_contents> | |
117 </output> | |
118 </test> | |
119 <test> | |
120 <param name="data_source|ref_data" value="RDP_v10"/> | |
121 <output name="out_file"> | |
122 <assert_contents> | |
123 <has_text text="16S rRNA RDP training set 10" /> | |
124 <has_text text="trainset10_082014.rdp.fasta" /> | |
125 <has_text text="trainset10_082014.rdp.tax" /> | |
126 <has_text text="trainset10_082014.pds.fasta" /> | |
127 <has_text text="trainset10_082014.pds.tax" /> | |
128 </assert_contents> | |
129 </output> | |
130 </test> | |
131 <test> | |
132 <param name="data_source|ref_data" value="RDP_v9"/> | |
133 <output name="out_file"> | |
134 <assert_contents> | |
135 <has_text text="16S rRNA PDS training set 9" /> | |
136 <has_text text="trainset9_032012.rdp.fasta" /> | |
137 <has_text text="trainset9_032012.rdp.tax" /> | |
138 <has_text text="trainset9_032012.pds.fasta" /> | |
139 <has_text text="trainset9_032012.pds.tax" /> | |
140 </assert_contents> | |
141 </output> | |
142 </test> | |
143 <test> | |
144 <param name="data_source|ref_data" value="RDP_v7"/> | |
145 <output name="out_file"> | |
146 <assert_contents> | |
147 <has_text text="16S rRNA RDP training set 7" /> | |
148 <has_text text="FungiLSU_train_1400bp_8506_mod.fasta" /> | |
149 <has_text text="FungiLSU_train_1400bp_8506_mod.tax" /> | |
150 <has_text text="trainset7_112011.rdp.fasta" /> | |
151 <has_text text="trainset7_112011.rdp.tax" /> | |
152 <has_text text="trainset7_112011.pds.fasta" /> | |
153 <has_text text="trainset7_112011.pds.tax" /> | |
154 </assert_contents> | |
155 </output> | |
156 </test> | |
157 <test> | |
158 <param name="data_source|ref_data" value="RDP_v6"/> | |
159 <output name="out_file"> | |
160 <assert_contents> | |
161 <has_text text="RDP training set 6" /> | |
162 <has_text text="trainset6_032010.rdp.fasta" /> | |
163 <has_text text="trainset6_032010.rdp.tax" /> | |
164 </assert_contents> | |
165 </output> | |
166 </test> | |
167 <!-- SILVA data is to large (>1GB each) for CI testing on github actions | |
168 so we skip them --> | |
169 <!--<test> | |
170 <param name="data_source|ref_data" value="silva_release_128"/> | |
171 <output name="out_file"> | |
172 <assert_contents> | |
173 <has_text text="SILVA release 128" /> | |
174 <has_text text="silva.nr_v128.tax" /> | |
175 <has_text text="silva.seed_v128.tax" /> | |
176 <has_text text="silva.nr_v128.align" /> | |
177 <has_text text="silva.seed_v128.align" /> | |
178 </assert_contents> | |
179 </output> | |
180 </test> | |
181 <test> | |
182 <param name="data_source|ref_data" value="silva_release_123"/> | |
183 <output name="out_file"> | |
184 <assert_contents> | |
185 <has_text text="SILVA release 123" /> | |
186 <has_text text="silva.nr_v123.align" /> | |
187 <has_text text="silva.seed_v123.align" /> | |
188 <has_text text="silva.nr_v123.tax" /> | |
189 <has_text text="silva.seed_v123.tax" /> | |
190 </assert_contents> | |
191 </output> | |
192 </test> | |
193 <test> | |
194 <param name="data_source|ref_data" value="silva_release_119"/> | |
195 <output name="out_file"> | |
196 <assert_contents> | |
197 <has_text text="SILVA release 119" /> | |
198 <has_text text="silva.nr_v119.align" /> | |
199 <has_text text="silva.seed_v119.align" /> | |
200 <has_text text="silva.nr_v119.tax" /> | |
201 <has_text text="silva.seed_v119.tax" /> | |
202 </assert_contents> | |
203 </output> | |
204 </test> | |
205 <test> | |
206 <param name="data_source|ref_data" value="silva_release_102"/> | |
207 <output name="out_file"> | |
208 <assert_contents> | |
209 <has_text text="SILVA release 102" /> | |
210 <has_text text="silva.bacteria.fasta" /> | |
211 <has_text text="silva.gold.ng.fasta" /> | |
212 <has_text text="nogap.archaea.fasta" /> | |
213 <has_text text="silva.archaea.fasta" /> | |
214 <has_text text="nogap.eukarya.fasta" /> | |
215 <has_text text="silva.eukarya.fasta" /> | |
216 <has_text text="silva.bacteria.gg.tax" /> | |
217 <has_text text="silva.bacteria.ncbi.tax" /> | |
218 <has_text text="silva.bacteria.rdp.tax" /> | |
219 <has_text text="silva.bacteria.rdp6.tax" /> | |
220 <has_text text="silva.bacteria.silva.tax" /> | |
221 <has_text text="silva.archaea.gg.tax" /> | |
222 <has_text text="silva.archaea.ncbi.tax" /> | |
223 <has_text text="silva.archaea.rdp.tax" /> | |
224 <has_text text="silva.archaea.silva.tax" /> | |
225 <has_text text="silva.eukarya.ncbi.tax" /> | |
226 <has_text text="silva.eukarya.silva.tax" /> | |
227 </assert_contents> | |
228 </output> | |
229 </test>--> | |
230 | |
231 <!-- also greengenes is large (400MB-1.5GB) so only tests for older | |
232 (smaller) releases are executed --> | |
233 <!--<test> | |
234 <param name="data_source|ref_data" value="greengenes_August2013"/> | |
235 <output name="out_file"> | |
236 <assert_contents> | |
237 <has_text text="Greengenes August 2013" /> | |
238 <has_text text="gg_13_8_99.gg.tax" /> | |
239 <has_text text="gg_13_8_99.fasta" /> | |
240 </assert_contents> | |
241 </output> | |
242 </test> | |
243 <test> | |
244 <param name="data_source|ref_data" value="greengenes_May2013"/> | |
245 <output name="out_file"> | |
246 <assert_contents> | |
247 <has_text text="Greengenes May 2013" /> | |
248 <has_text text="gg_13_5_99.pds.tax" /> | |
249 <has_text text="gg_13_5_99.gg.tax" /> | |
250 <has_text text="gg_13_5_99.align" /> | |
251 <has_text text="gg_13_5_99.fasta" /> | |
252 </assert_contents> | |
253 </output> | |
254 </test>--> | |
255 <test> | |
256 <param name="data_source|ref_data" value="greengenes_old"/> | |
257 <output name="out_file"> | |
258 <assert_contents> | |
259 <has_text text="Greengenes pre-May 2013" /> | |
260 <has_text text="gg_99.pds.tax" /> | |
261 <has_text text="core_set_aligned.imputed.fasta" /> | |
262 <has_text text="gg_99.pds.ng.fasta" /> | |
263 </assert_contents> | |
264 </output> | |
265 </test> | |
266 <test> | |
267 <param name="data_source|ref_data" value="greengenes_gold_alignment"/> | |
268 <output name="out_file"> | |
269 <assert_contents> | |
270 <has_text text="Greengenes gold alignment" /> | |
271 <has_text text="rRNA16S.gold.NAST_ALIGNED.fasta" /> | |
272 </assert_contents> | |
273 </output> | |
274 </test> | |
275 | |
276 <test> | |
277 <param name="data_source|ref_data" value="secondary_structure_maps_silva"/> | |
278 <output name="out_file"> | |
279 <assert_contents> | |
280 <has_text text="SILVA" /> | |
281 <has_text text="silva.ss.map" /> | |
282 </assert_contents> | |
283 </output> | |
284 </test> | |
285 <test> | |
286 <param name="data_source|ref_data" value="secondary_structure_maps_greengenes"/> | |
287 <output name="out_file"> | |
288 <assert_contents> | |
289 <has_text text="Greengenes" /> | |
290 <has_text text="gg.ss.map" /> | |
291 </assert_contents> | |
292 </output> | |
293 </test> | |
77 </tests> | 294 </tests> |
78 <help> | 295 <help> |
79 .. class:: infomark | 296 .. class:: infomark |
80 | 297 |
81 **What it does** | 298 **What it does** |