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comparison data_manager/kraken2_build_database.xml @ 10:13851aefa67a 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 ea1cf7593dd429e0f6272f9cf3d08cd3a46b6235
author iuc
date Thu, 13 Jun 2024 12:18:58 +0000
parents 539b008cfe1c
children 1e34d2e3d285
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9:539b008cfe1c 10:13851aefa67a
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 <description>database builder</description>
4 <macros> 4 <macros>
5 <token name="@TOOL_VERSION@">2.1.3</token> 5 <token name="@TOOL_VERSION@">2.1.3</token>
6 <token name="@VERSION_SUFFIX@">0</token> 6 <token name="@VERSION_SUFFIX@">1</token>
7 <token name="@PROFILE@">22.01</token> 7 <token name="@PROFILE@">22.01</token>
8 <xml name="common_params"> 8 <xml name="common_params">
9 <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" />
10 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> 10 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
11 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> 11 <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" />
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="2024-12-01">December 1, 2024</option> 106 <option value="2024-01-12">January 12, 2024</option>
107 <option value="2023-06-05">June 5, 2023</option> 107 <option value="2023-06-05">June 5, 2023</option>
108 <option value="2022-06-07">June 7, 2022</option> 108 <option value="2022-06-07">June 7, 2022</option>
109 <option value="2021-05-17">May 17, 2021</option> 109 <option value="2021-05-17">May 17, 2021</option>
110 <option value="2021-01-27">January 27, 2021</option> 110 <option value="2021-01-27">January 27, 2021</option>
111 <option value="2020-12-02">December 2, 2020</option> 111 <option value="2020-12-02">December 2, 2020</option>
112 <option value="2020-09-19">September 19, 2020</option> 112 <option value="2020-09-19">September 19, 2020</option>
113 </param> 113 </param>
114 <when value="2024-12-01"> 114 <when value="2024-01-12">
115 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> 115 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
116 <expand macro="viral"/> 116 <expand macro="viral"/>
117 <expand macro="minusb"/> 117 <expand macro="minusb"/>
118 <expand macro="standard"/> 118 <expand macro="standard"/>
119 <expand macro="standard_08gb"/> 119 <expand macro="standard_08gb"/>
265 <has_text text="Version"/> 265 <has_text text="Version"/>
266 <has_text text="Downloaded"/> 266 <has_text text="Downloaded"/>
267 </assert_contents> 267 </assert_contents>
268 </output> 268 </output>
269 </test> 269 </test>
270 <!-- test with latest version -->
271 <test>
272 <conditional name="database_type">
273 <param name="database_type" value="standard_prebuilt" />
274 <conditional name="prebuild">
275 <param name="prebuilt_date" value="2024-01-12"/>
276 <param name="prebuilt_db" value="viral"/>
277 </conditional>
278 </conditional>
279 <output name="out_file">
280 <assert_contents>
281 <has_text text="kraken2_databases"/>
282 <has_text text="path"/>
283 <has_text text="Viral"/>
284 <has_text text="_standard_prebuilt_viral_2024-01-12"/>
285 <has_text text="Version"/>
286 <has_text text="Downloaded"/>
287 </assert_contents>
288 </output>
289 </test>
270 </tests> 290 </tests>
271 <help><![CDATA[ 291 <help><![CDATA[
272 Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__ 292 Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
273 ]]></help> 293 ]]></help>
274 <citations> 294 <citations>