Mercurial > repos > iuc > data_manager_build_kraken2_database

comparison data_manager/kraken2_build_database.xml @ 11:36cdd9783e6b 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 66be7bc4e07926c3645ba87f78702f2267fad7b3
author iuc
date Fri, 13 Dec 2024 21:18:22 +0000
parents 4726ecf3b61b
children bf7f964a12b7
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equal deleted inserted replaced
10:4726ecf3b61b 11:36cdd9783e6b
1 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>database builder</description> 2 <description>database builder</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.1.3</token> 4 <token name="@TOOL_VERSION@">2.1.3</token>
5 <token name="@VERSION_SUFFIX@">4</token> 5 <token name="@VERSION_SUFFIX@">5</token>
6 <token name="@PROFILE@">22.01</token> 6 <token name="@PROFILE@">22.01</token>
7 <xml name="common_params"> 7 <xml name="common_params">
8 <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> 8 <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" /> 9 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
10 <param name="minimizer_spaces" type="integer" value="7" label="Minimizer spaces" /> 10 <param name="minimizer_spaces" type="integer" value="7" label="Minimizer spaces" />
41 <xml name="pluspfp_08gb"> 41 <xml name="pluspfp_08gb">
42 <option value="pluspfp_08gb">PlusPFP-8 (PlusPFP with DB capped at 8 GB; ~7.5 GB)</option> 42 <option value="pluspfp_08gb">PlusPFP-8 (PlusPFP with DB capped at 8 GB; ~7.5 GB)</option>
43 </xml> 43 </xml>
44 <xml name="pluspfp_16gb"> 44 <xml name="pluspfp_16gb">
45 <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option> 45 <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
46 </xml>
47 <xml name="core_nt">
48 <option value="core_nt">core_nt (Very large collection, inclusive of GenBank, RefSeq, TPA and PDB; ~182 GB)</option>
46 </xml> 49 </xml>
47 </macros> 50 </macros>
48 <xrefs> 51 <xrefs>
49 <xref type="bio.tools">kraken2</xref> 52 <xref type="bio.tools">kraken2</xref>
50 </xrefs> 53 </xrefs>
108 <expand macro="common_params" /> 111 <expand macro="common_params" />
109 </when> 112 </when>
110 <when value="standard_prebuilt"> 113 <when value="standard_prebuilt">
111 <conditional name="prebuild"> 114 <conditional name="prebuild">
112 <param name="prebuilt_date" type="select" label="Select index build date"> 115 <param name="prebuilt_date" type="select" label="Select index build date">
116 <option value="2024-09-04">September 4, 2024</option>
113 <option value="2024-06-05">June 5, 2024</option> 117 <option value="2024-06-05">June 5, 2024</option>
114 <option value="2024-01-12">January 12, 2024</option> 118 <option value="2024-01-12">January 12, 2024</option>
115 <option value="2023-06-05">June 5, 2023</option> 119 <option value="2023-06-05">June 5, 2023</option>
116 <option value="2022-06-07">June 7, 2022</option> 120 <option value="2022-06-07">June 7, 2022</option>
117 <option value="2021-05-17">May 17, 2021</option> 121 <option value="2021-05-17">May 17, 2021</option>
118 <option value="2021-01-27">January 27, 2021</option> 122 <option value="2021-01-27">January 27, 2021</option>
119 <option value="2020-12-02">December 2, 2020</option> 123 <option value="2020-12-02">December 2, 2020</option>
120 <option value="2020-09-19">September 19, 2020</option> 124 <option value="2020-09-19">September 19, 2020</option>
121 </param> 125 </param>
126 <when value="2024-09-04">
127 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
128 <expand macro="viral"/>
129 <expand macro="minusb"/>
130 <expand macro="standard"/>
131 <expand macro="standard_08gb"/>
132 <expand macro="standard_16gb"/>
133 <expand macro="pluspf"/>
134 <expand macro="pluspf_08gb"/>
135 <expand macro="pluspf_16gb"/>
136 <expand macro="pluspfp"/>
137 <expand macro="pluspfp_08gb"/>
138 <expand macro="core_nt"/>
139 </param>
140 </when>
122 <when value="2024-06-05"> 141 <when value="2024-06-05">
123 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download"> 142 <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
124 <expand macro="viral"/> 143 <expand macro="viral"/>
125 <expand macro="minusb"/> 144 <expand macro="minusb"/>
126 <expand macro="standard"/> 145 <expand macro="standard"/>
227 </conditional> 246 </conditional>
228 </when> 247 </when>
229 <when value="special_prebuilt"> 248 <when value="special_prebuilt">
230 <conditional name="special_prebuild"> 249 <conditional name="special_prebuild">
231 <param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download"> 250 <param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download">
232 <option value="eupathdb48_20230407">EuPathDB-46 (April 7, 2023)</option> 251 <option value="gtdb_genome_reps_20241109">GTDB v220 (Bacterial and archaeal; ~497 GB) (December 13, 2024)</option>
252 <option value="eupathdb48_20230407">EuPathDB-46 (April 18, 2023)</option>
233 <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option> 253 <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
234 </param> 254 </param>
255 <when value="gtdb_genome_reps_20241109">
256 <param name="prebuilt_db" type="hidden" value="gtdb_genome_reps"/>
257 <param name="prebuilt_date" type="hidden" value="2024-11-09"/>
258 </when>
235 <when value="eupathdb48_20230407"> 259 <when value="eupathdb48_20230407">
236 <param name="prebuilt_db" type="hidden" value="eupathdb48"/> 260 <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
237 <param name="prebuilt_date" type="hidden" value="2023-04-07"/> 261 <param name="prebuilt_date" type="hidden" value="2023-04-07"/>
238 </when> 262 </when>
239 <when value="eupathdb48_20201113"> 263 <when value="eupathdb48_20201113">