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comparison data_manager/kraken2_build_database.xml @ 8:1108eae823a8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit efa1fd42c2a5a618bd628ff435e5dde1c1ef3545
author iuc
date Mon, 15 Jul 2024 09:21:25 +0000
parents 691a1055a112
children ba981d05e216
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7:ce75e9475f0f 8:1108eae823a8
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 2 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>database builder</description>
3 <macros> 4 <macros>
4 <token name="@TOOL_VERSION@">2.1.2</token> 5 <token name="@TOOL_VERSION@">2.1.3</token>
5 <token name="@VERSION_SUFFIX@">0</token> 6 <token name="@VERSION_SUFFIX@">2</token>
6 <token name="@PROFILE@">21.01</token> 7 <token name="@PROFILE@">22.01</token>
7 <xml name="common_params"> 8 <xml name="common_params">
8 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> 9 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
9 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> 10 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
10 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> 11 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
11 <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" /> 12 <param name="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" />
12 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" /> 13 <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
13 </xml> 14 </xml>
14 <xml name="viral"> 15 <xml name="viral">
15 <option value="viral">Viral (viral; ~50 GB)</option> 16 <option value="viral">Viral (viral; ~0.5 GB)</option>
16 </xml> 17 </xml>
17 <xml name="minusb"> 18 <xml name="minusb">
18 <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option> 19 <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option>
19 </xml> 20 </xml>
20 <xml name="standard"> 21 <xml name="standard">
43 </xml> 44 </xml>
44 <xml name="pluspfp_16gb"> 45 <xml name="pluspfp_16gb">
45 <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option> 46 <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
46 </xml> 47 </xml>
47 </macros> 48 </macros>
48 <description>database builder</description>
49 <requirements> 49 <requirements>
50 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> 50 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
51 <requirement type="package" version="3.7">python</requirement> 51 <requirement type="package" version="3.7">python</requirement>
52 </requirements> 52 </requirements>
53 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> 53 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
101 <expand macro="common_params" /> 101 <expand macro="common_params" />
102 </when> 102 </when>
103 <when value="standard_prebuilt"> 103 <when value="standard_prebuilt">
104 <conditional name="prebuild"> 104 <conditional name="prebuild">
105 <param name="prebuilt_date" type="select" label="Select index build date"> 105 <param name="prebuilt_date" type="select" label="Select index build date">
106 <option value="2024-06-05">June 5, 2024</option>
107 <option value="2024-01-12">January 12, 2024</option>
108 <option value="2023-06-05">June 5, 2023</option>
106 <option value="2022-06-07">June 7, 2022</option> 109 <option value="2022-06-07">June 7, 2022</option>
107 <option value="2021-05-17">May 17, 2021</option> 110 <option value="2021-05-17">May 17, 2021</option>
108 <option value="2021-01-27">January 27, 2021</option> 111 <option value="2021-01-27">January 27, 2021</option>
109 <option value="2020-12-02">December 2, 2020</option> 112 <option value="2020-12-02">December 2, 2020</option>
110 <option value="2020-09-19">September 19, 2020</option> 113 <option value="2020-09-19">September 19, 2020</option>
111 </param> 114 </param>
115 <when value="2024-06-05">
116 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
117 <expand macro="viral"/>
118 <expand macro="minusb"/>
119 <expand macro="standard"/>
120 <expand macro="standard_08gb"/>
121 <expand macro="standard_16gb"/>
122 <expand macro="pluspf"/>
123 <expand macro="pluspf_08gb"/>
124 <expand macro="pluspf_16gb"/>
125 <expand macro="pluspfp"/>
126 <expand macro="pluspfp_08gb"/>
127 <expand macro="pluspfp_16gb"/>
128 </param>
129 </when>
130 <when value="2024-01-12">
131 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
132 <expand macro="viral"/>
133 <expand macro="minusb"/>
134 <expand macro="standard"/>
135 <expand macro="standard_08gb"/>
136 <expand macro="standard_16gb"/>
137 <expand macro="pluspf"/>
138 <expand macro="pluspf_08gb"/>
139 <expand macro="pluspf_16gb"/>
140 <expand macro="pluspfp"/>
141 <expand macro="pluspfp_08gb"/>
142 <expand macro="pluspfp_16gb"/>
143 </param>
144 </when>
145 <when value="2023-06-05">
146 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
147 <expand macro="viral"/>
148 <expand macro="minusb"/>
149 <expand macro="standard"/>
150 <expand macro="standard_08gb"/>
151 <expand macro="standard_16gb"/>
152 <expand macro="pluspf"/>
153 <expand macro="pluspf_08gb"/>
154 <expand macro="pluspf_16gb"/>
155 <expand macro="pluspfp"/>
156 <expand macro="pluspfp_08gb"/>
157 <expand macro="pluspfp_16gb"/>
158 </param>
159 </when>
112 <when value="2022-06-07"> 160 <when value="2022-06-07">
113 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> 161 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
114 <expand macro="viral"/> 162 <expand macro="viral"/>
115 <expand macro="minusb"/> 163 <expand macro="minusb"/>
116 <expand macro="standard"/> 164 <expand macro="standard"/>
204 <param name="custom_database_name" value="custom_database" /> 252 <param name="custom_database_name" value="custom_database" />
205 <param name="skip_maps" value="true" /> 253 <param name="skip_maps" value="true" />
206 <param name="kmer_len" value="35" /> 254 <param name="kmer_len" value="35" />
207 <param name="minimizer_spaces" value="6"/> 255 <param name="minimizer_spaces" value="6"/>
208 <param name="load_factor" value="0.7" /> 256 <param name="load_factor" value="0.7" />
209 <param name="clean" truevalue="--clean"/> 257 <param name="clean" value="true"/>
210 </conditional> 258 </conditional>
211 <output name="out_file"> 259 <output name="out_file">
212 <assert_contents> 260 <assert_contents>
213 <has_text text="kraken2_databases"/> 261 <has_text text="kraken2_databases"/>
214 <has_text text="path"/> 262 <has_text text="path"/>
219 <test> 267 <test>
220 <conditional name="database_type"> 268 <conditional name="database_type">
221 <param name="database_type" value="standard_prebuilt" /> 269 <param name="database_type" value="standard_prebuilt" />
222 <conditional name="prebuild"> 270 <conditional name="prebuild">
223 <param name="prebuilt_date" value="2022-06-07"/> 271 <param name="prebuilt_date" value="2022-06-07"/>
224 <param name="prebuilt_db" value="standard_08gb"/> 272 <param name="prebuilt_db" value="viral"/>
225 </conditional> 273 </conditional>
226 </conditional> 274 </conditional>
227 <output name="out_file"> 275 <output name="out_file">
228 <assert_contents> 276 <assert_contents>
229 <has_text text="kraken2_databases"/> 277 <has_text text="kraken2_databases"/>
230 <has_text text="path"/> 278 <has_text text="path"/>
231 <has_text text="Standard-8"/> 279 <has_text text="Viral"/>
232 <has_text text="_standard_prebuilt_standard_08gb_2022-06-07"/> 280 <has_text text="_standard_prebuilt_viral_2022-06-07"/>
281 <has_text text="Version"/>
282 <has_text text="Downloaded"/>
283 </assert_contents>
284 </output>
285 </test>
286 <!-- test with latest version -->
287 <test>
288 <conditional name="database_type">
289 <param name="database_type" value="standard_prebuilt" />
290 <conditional name="prebuild">
291 <param name="prebuilt_date" value="2024-01-12"/>
292 <param name="prebuilt_db" value="viral"/>
293 </conditional>
294 </conditional>
295 <output name="out_file">
296 <assert_contents>
297 <has_text text="kraken2_databases"/>
298 <has_text text="path"/>
299 <has_text text="Viral"/>
300 <has_text text="_standard_prebuilt_viral_2024-01-12"/>
301 <has_text text="Version"/>
302 <has_text text="Downloaded"/>
303 </assert_contents>
304 </output>
305 </test>
306 <!-- test with first 2024 version -->
307 <test>
308 <conditional name="database_type">
309 <param name="database_type" value="standard_prebuilt" />
310 <conditional name="prebuild">
311 <param name="prebuilt_date" value="2024-06-05"/>
312 <param name="prebuilt_db" value="viral"/>
313 </conditional>
314 </conditional>
315 <output name="out_file">
316 <assert_contents>
317 <has_text text="kraken2_databases"/>
318 <has_text text="path"/>
319 <has_text text="Viral"/>
320 <has_text text="_standard_prebuilt_viral_2024-06-05"/>
233 <has_text text="Version"/> 321 <has_text text="Version"/>
234 <has_text text="Downloaded"/> 322 <has_text text="Downloaded"/>
235 </assert_contents> 323 </assert_contents>
236 </output> 324 </output>
237 </test> 325 </test>