Mercurial > repos > iuc > data_manager_build_kraken2_database

comparison data_manager/kraken2_build_database.xml @ 10:4726ecf3b61b 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 bb6d9b53b197610c5dbbb40c8ab590761755d91a
author iuc
date Fri, 15 Nov 2024 22:31:20 +0000
parents ba981d05e216
children 36cdd9783e6b
comparison
equal deleted inserted replaced
9:ba981d05e216 10:4726ecf3b61b
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@"> 1 <tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>database builder</description> 2 <description>database builder</description>
4 <macros> 3 <macros>
5 <token name="@TOOL_VERSION@">2.1.3</token> 4 <token name="@TOOL_VERSION@">2.1.3</token>
6 <token name="@VERSION_SUFFIX@">3</token> 5 <token name="@VERSION_SUFFIX@">4</token>
7 <token name="@PROFILE@">22.01</token> 6 <token name="@PROFILE@">22.01</token>
8 <xml name="common_params"> 7 <xml name="common_params">
9 <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" />
10 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> 9 <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
11 <param name="minimizer_spaces" type="integer" value="7" label="Minimizer spaces" /> 10 <param name="minimizer_spaces" type="integer" value="7" label="Minimizer spaces" />
68 #else if $database_type.database_type == "standard_prebuilt" 67 #else if $database_type.database_type == "standard_prebuilt"
69 --prebuilt-db '$database_type.prebuild.prebuilt_db' 68 --prebuilt-db '$database_type.prebuild.prebuilt_db'
70 --prebuilt-date '$database_type.prebuild.prebuilt_date' 69 --prebuilt-date '$database_type.prebuild.prebuilt_date'
71 #else if $database_type.database_type == "minikraken" 70 #else if $database_type.database_type == "minikraken"
72 --minikraken2-version '$database_type.minikraken2_version' 71 --minikraken2-version '$database_type.minikraken2_version'
72 #else if $database_type.database_type == "special_prebuilt"
73 --prebuilt-db '$database_type.special_prebuild.prebuilt_db'
74 --prebuilt-date '$database_type.special_prebuild.prebuilt_date'
73 #else if $database_type.database_type == "special" 75 #else if $database_type.database_type == "special"
74 --threads \${GALAXY_SLOTS:-1} 76 --threads \${GALAXY_SLOTS:-1}
75 --special-database-type '$database_type.special_database_type' 77 --special-database-type '$database_type.special_database_type'
76 --kmer-len $database_type.kmer_len 78 --kmer-len $database_type.kmer_len
77 --minimizer-len $database_type.minimizer_len 79 --minimizer-len $database_type.minimizer_len
96 <conditional name="database_type"> 98 <conditional name="database_type">
97 <param name="database_type" type="select" multiple="false" label="Database Type"> 99 <param name="database_type" type="select" multiple="false" label="Database Type">
98 <option value="standard_local_build">Standard, Local Build</option> 100 <option value="standard_local_build">Standard, Local Build</option>
99 <option value="standard_prebuilt">Pre-Built Refseq indexes</option> 101 <option value="standard_prebuilt">Pre-Built Refseq indexes</option>
100 <option value="minikraken">MiniKraken</option> 102 <option value="minikraken">MiniKraken</option>
103 <option value="special_prebuilt">Special Pre-Built indexes</option>
101 <option value="special">Special</option> 104 <option value="special">Special</option>
102 <option value="custom">Custom</option> 105 <option value="custom">Custom</option>
103 </param> 106 </param>
104 <when value="standard_local_build"> 107 <when value="standard_local_build">
105 <expand macro="common_params" /> 108 <expand macro="common_params" />
218 <expand macro="pluspf_08gb"/> 221 <expand macro="pluspf_08gb"/>
219 <expand macro="pluspf_16gb"/> 222 <expand macro="pluspf_16gb"/>
220 <expand macro="pluspfp_08gb"/> 223 <expand macro="pluspfp_08gb"/>
221 <expand macro="pluspfp_16gb"/> 224 <expand macro="pluspfp_16gb"/>
222 </param> 225 </param>
226 </when>
227 </conditional>
228 </when>
229 <when value="special_prebuilt">
230 <conditional name="special_prebuild">
231 <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>
233 <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
234 </param>
235 <when value="eupathdb48_20230407">
236 <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
237 <param name="prebuilt_date" type="hidden" value="2023-04-07"/>
238 </when>
239 <when value="eupathdb48_20201113">
240 <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
241 <param name="prebuilt_date" type="hidden" value="2020-11-13"/>
223 </when> 242 </when>
224 </conditional> 243 </conditional>
225 </when> 244 </when>
226 <when value="minikraken"> 245 <when value="minikraken">
227 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> 246 <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">