Mercurial > repos > iuc > data_manager_build_kraken2_database

comparison data_manager/kraken2_build_database.xml @ 8:e4b4837f06f5 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 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author iuc
date Mon, 18 Dec 2023 09:36:03 +0000
parents 9002633b4737
children 539b008cfe1c
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7:ed1518ce2237 8:e4b4837f06f5
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@">2.1.2</token>
5 <token name="@VERSION_SUFFIX@">0</token> 6 <token name="@VERSION_SUFFIX@">1</token>
6 <token name="@PROFILE@">21.01</token> 7 <token name="@PROFILE@">21.01</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" />
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>
204 <param name="custom_database_name" value="custom_database" /> 204 <param name="custom_database_name" value="custom_database" />
205 <param name="skip_maps" value="true" /> 205 <param name="skip_maps" value="true" />
206 <param name="kmer_len" value="35" /> 206 <param name="kmer_len" value="35" />
207 <param name="minimizer_spaces" value="6"/> 207 <param name="minimizer_spaces" value="6"/>
208 <param name="load_factor" value="0.7" /> 208 <param name="load_factor" value="0.7" />
209 <param name="clean" truevalue="--clean"/> 209 <param name="clean" value="true"/>
210 </conditional> 210 </conditional>
211 <output name="out_file"> 211 <output name="out_file">
212 <assert_contents> 212 <assert_contents>
213 <has_text text="kraken2_databases"/> 213 <has_text text="kraken2_databases"/>
214 <has_text text="path"/> 214 <has_text text="path"/>