Mercurial > repos > iuc > data_manager_build_kraken2_database

comparison data_manager/kraken2_build_database.xml @ 9:ba981d05e216 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 9835da32741d05d129a1a44835f66e32713770ad
author iuc
date Fri, 18 Oct 2024 17:08:05 +0000
parents 1108eae823a8
children 4726ecf3b61b
comparison
equal deleted inserted replaced
8:1108eae823a8 9:ba981d05e216
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@">2</token> 6 <token name="@VERSION_SUFFIX@">3</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="7" label="Minimizer spaces" />
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="load_factor" type="float" value="0.7" min="0" max="1" label="Load factor" help="Proportion of the hash table to be populated" />
13 <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" />
14 </xml> 14 </xml>
15 <xml name="viral"> 15 <xml name="viral">
16 <option value="viral">Viral (viral; ~0.5 GB)</option> 16 <option value="viral">Viral (viral; ~0.5 GB)</option>
44 </xml> 44 </xml>
45 <xml name="pluspfp_16gb"> 45 <xml name="pluspfp_16gb">
46 <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>
47 </xml> 47 </xml>
48 </macros> 48 </macros>
49 <xrefs>
50 <xref type="bio.tools">kraken2</xref>
51 </xrefs>
49 <requirements> 52 <requirements>
50 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> 53 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
51 <requirement type="package" version="3.7">python</requirement> 54 <requirement type="package" version="3.13">python</requirement>
52 </requirements> 55 </requirements>
53 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> 56 <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
54 <command detect_errors="exit_code"><![CDATA[ 57 <command detect_errors="exit_code"><![CDATA[
55 python '$__tool_directory__/kraken2_build_database.py' 58 python '$__tool_directory__/kraken2_build_database.py'
56 '$out_file' 59 '$out_file'
77 $database_type.clean 80 $database_type.clean
78 #else if $database_type.database_type == "custom" 81 #else if $database_type.database_type == "custom"
79 --threads \${GALAXY_SLOTS:-1} 82 --threads \${GALAXY_SLOTS:-1}
80 --custom-fasta '$database_type.custom_fasta' 83 --custom-fasta '$database_type.custom_fasta'
81 --custom-database-name '$database_type.custom_database_name' 84 --custom-database-name '$database_type.custom_database_name'
85 --custom-source-info '$database_type.custom_source_info'
82 $database_type.skip_maps 86 $database_type.skip_maps
83 --kmer-len $database_type.kmer_len 87 --kmer-len $database_type.kmer_len
84 --minimizer-len $database_type.minimizer_len 88 --minimizer-len $database_type.minimizer_len
85 --minimizer-spaces $database_type.minimizer_spaces 89 --minimizer-spaces $database_type.minimizer_spaces
86 --load-factor $database_type.load_factor 90 --load-factor $database_type.load_factor
234 <expand macro="common_params" /> 238 <expand macro="common_params" />
235 </when> 239 </when>
236 <when value="custom"> 240 <when value="custom">
237 <param name="custom_fasta" type="data" format="fasta" multiple="False" label="Select history item" /> 241 <param name="custom_fasta" type="data" format="fasta" multiple="False" label="Select history item" />
238 <param name="custom_database_name" type="text" label="Name for this database" /> 242 <param name="custom_database_name" type="text" label="Name for this database" />
243 <param name="custom_source_info" type="text" label="Database source info" help="Concise description of how this build has been sourced. This description will be appended (in parentheses) to the user-facing name of the build. Example: https://doi.org/10.5281/zenodo.8339822, from v1 assembly_summary.txt sequences" />
239 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." /> 244 <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." />
240 <expand macro="common_params" /> 245 <expand macro="common_params" />
241 </when> 246 </when>
242 </conditional> 247 </conditional>
243 </inputs> 248 </inputs>
248 <test expect_num_outputs="1"> 253 <test expect_num_outputs="1">
249 <conditional name="database_type"> 254 <conditional name="database_type">
250 <param name="database_type" value="custom" /> 255 <param name="database_type" value="custom" />
251 <param name="custom_fasta" value="adapter.fa" /> 256 <param name="custom_fasta" value="adapter.fa" />
252 <param name="custom_database_name" value="custom_database" /> 257 <param name="custom_database_name" value="custom_database" />
258 <param name="custom_source_info" value="from adapter.fa test data" />
253 <param name="skip_maps" value="true" /> 259 <param name="skip_maps" value="true" />
254 <param name="kmer_len" value="35" /> 260 <param name="kmer_len" value="35" />
255 <param name="minimizer_spaces" value="6"/> 261 <param name="minimizer_spaces" value="6"/>
256 <param name="load_factor" value="0.7" /> 262 <param name="load_factor" value="0.7" />
257 <param name="clean" value="true"/> 263 <param name="clean" value="true"/>
258 </conditional> 264 </conditional>
259 <output name="out_file"> 265 <output name="out_file">
260 <assert_contents> 266 <assert_contents>
261 <has_text text="kraken2_databases"/> 267 <has_text text="kraken2_databases"/>
262 <has_text text="path"/> 268 <has_text text="path"/>
263 <has_text text="custom_database"/> 269 <has_text text="custom_database (from adapter.fa test data, kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7)"/>
264 </assert_contents> 270 </assert_contents>
265 </output> 271 </output>
266 </test> 272 </test>
267 <test> 273 <test>
268 <conditional name="database_type"> 274 <conditional name="database_type">
326 </tests> 332 </tests>
327 <help><![CDATA[ 333 <help><![CDATA[
328 Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__ 334 Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
329 ]]></help> 335 ]]></help>
330 <citations> 336 <citations>
331 <citation type="doi">10.1186/gb-2014-15-3-r46</citation> 337 <citation type="doi">10.1186/s13059-019-1891-0</citation>
332 </citations> 338 </citations>
333 </tool> 339 </tool>