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comparison data_manager/data_manager_fetch_mothur_reference_data.xml @ 2:0e532fc0a0a6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309"
author iuc
date Thu, 17 Sep 2020 09:37:41 +0000
parents aec831b54a5b
children 0db22932bc39
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1:aec831b54a5b 2:0e532fc0a0a6
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**