diff data_manager/kraken2_build_database.xml @ 0:c13785ca6192 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 39e87c095e426fc3f147d55de0434cd54ae0354a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/kraken2_build_database.xml	Wed Nov 06 20:00:39 2024 +0000
@@ -0,0 +1,359 @@
+<?xml version="1.0"?>
+<tool id="kraken2_build_database" name="Kraken2" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>database builder</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.1.3</token>
+        <token name="@VERSION_SUFFIX@">3</token>
+        <token name="@PROFILE@">22.01</token>
+        <xml name="common_params">
+            <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" />
+            <param name="minimizer_len" type="integer" value="31" label="Minimizer length" />
+            <param name="minimizer_spaces" type="integer" value="7" label="Minimizer spaces" />
+            <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" />
+            <param name="clean" type="boolean" truevalue="--clean" falsevalue="" checked="true" label="Clean up extra files" />
+        </xml>
+        <xml name="viral">
+            <option value="viral">Viral (viral; ~0.5 GB)</option>
+        </xml>
+        <xml name="minusb">
+            <option value="minusb">MinusB (archaea, viral, plasmid, human, UniVec_Core; ~8 GB)</option>
+        </xml>
+        <xml name="standard">
+            <option value="standard">Standard-Full (archaea, bacteria, viral, plasmid, human, UniVec_Core; ~50 GB)</option>
+        </xml>
+        <xml name="standard_08gb">
+            <option value="standard_08gb">Standard-8 (Standard with DB capped at 8 GB)</option>
+        </xml>
+        <xml name="standard_16gb">
+            <option value="standard_16gb">Standard-16 (Standard with DB capped at 16 GB)</option>
+        </xml>
+        <xml name="pluspf">
+            <option value="pluspf">PlusPF (Standard plus protozoa and fungi; ~50 GB)</option>
+        </xml>
+        <xml name="pluspf_08gb">
+            <option value="pluspf_08gb">PlusPF-8 (PlusPF with DB capped at 8 GB; ~7.5 GB)</option>
+        </xml>
+        <xml name="pluspf_16gb">
+            <option value="pluspf_16gb">PlusPF-16 (PlusPF with DB capped at 16 GB; ~15 GB)</option>
+        </xml>
+        <xml name="pluspfp">
+            <option value="pluspfp">PlusPFP (Standard plus protozoa, fungi and plant; ~129 GB)</option>
+        </xml>
+        <xml name="pluspfp_08gb">
+            <option value="pluspfp_08gb">PlusPFP-8 (PlusPFP with DB capped at 8 GB; ~7.5 GB)</option>
+        </xml>
+        <xml name="pluspfp_16gb">
+            <option value="pluspfp_16gb">PlusPFP-16 (PlusPFP with DB capped at 16 GB; ~15 GB)</option>
+        </xml>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">kraken2</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
+        <requirement type="package" version="3.13">python</requirement>
+    </requirements>
+    <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/kraken2_build_database.py'
+    '$out_file'
+    --database-type '$database_type.database_type'
+#if $database_type.database_type == "standard_local_build"
+    --threads \${GALAXY_SLOTS:-1}
+    --kmer-len $database_type.kmer_len
+    --minimizer-len $database_type.minimizer_len
+    --minimizer-spaces $database_type.minimizer_spaces
+    --load-factor $database_type.load_factor
+    $database_type.clean
+#else if $database_type.database_type == "standard_prebuilt"
+    --prebuilt-db '$database_type.prebuild.prebuilt_db'
+    --prebuilt-date '$database_type.prebuild.prebuilt_date'
+#else if $database_type.database_type == "minikraken"
+    --minikraken2-version '$database_type.minikraken2_version'
+#else if $database_type.database_type == "special_prebuilt"
+    --prebuilt-db '$database_type.special_prebuild.prebuilt_db'
+    --prebuilt-date '$database_type.special_prebuild.prebuilt_date'
+#else if $database_type.database_type == "special"
+    --threads \${GALAXY_SLOTS:-1}
+    --special-database-type '$database_type.special_database_type'
+    --kmer-len $database_type.kmer_len
+    --minimizer-len $database_type.minimizer_len
+    --minimizer-spaces $database_type.minimizer_spaces
+    --load-factor $database_type.load_factor
+    $database_type.clean
+#else if $database_type.database_type == "custom"
+    --threads \${GALAXY_SLOTS:-1}
+    --custom-fasta '$database_type.custom_fasta'
+    --custom-database-name '$database_type.custom_database_name'
+    --custom-source-info '$database_type.custom_source_info'
+    $database_type.skip_maps
+    --kmer-len $database_type.kmer_len
+    --minimizer-len $database_type.minimizer_len
+    --minimizer-spaces $database_type.minimizer_spaces
+    --load-factor $database_type.load_factor
+    $database_type.clean
+#end if
+]]>
+    </command>
+    <inputs>
+        <conditional name="database_type">
+            <param name="database_type" type="select" multiple="false" label="Database Type">
+                <option value="standard_local_build">Standard, Local Build</option>
+                <option value="standard_prebuilt">Pre-Built Refseq indexes</option>
+                <option value="minikraken">MiniKraken</option>
+                <option value="special_prebuilt">Special Pre-Built indexes</option>
+                <option value="special">Special</option>
+                <option value="custom">Custom</option>
+            </param>
+            <when value="standard_local_build">
+                <expand macro="common_params" />
+            </when>
+            <when value="standard_prebuilt">
+                <conditional name="prebuild">
+                    <param name="prebuilt_date" type="select" label="Select index build date">
+                        <option value="2024-06-05">June 5, 2024</option>
+                        <option value="2024-01-12">January 12, 2024</option>
+                        <option value="2023-06-05">June 5, 2023</option>
+                        <option value="2022-06-07">June 7, 2022</option>
+                        <option value="2021-05-17">May 17, 2021</option>
+                        <option value="2021-01-27">January 27, 2021</option>
+                        <option value="2020-12-02">December 2, 2020</option>
+                        <option value="2020-09-19">September 19, 2020</option>
+                    </param>
+                    <when value="2024-06-05">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2024-01-12">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2023-06-05">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2022-06-07">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2021-05-17">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2021-01-27">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2020-12-02">
+                        <param name="prebuilt_db" type="select" label="Select a prebuilt Refseq index to download">
+                            <expand macro="viral"/>
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                        </param>
+                    </when>
+                    <when value="2020-09-19">
+                        <param name="prebuilt_db" type="select" multiple="false" label="Select a prebuilt Refseq indexes to download">
+                            <expand macro="minusb"/>
+                            <expand macro="standard"/>
+                            <expand macro="standard_08gb"/>
+                            <expand macro="standard_16gb"/>
+                            <expand macro="pluspf"/>
+                            <expand macro="pluspf_08gb"/>
+                            <expand macro="pluspf_16gb"/>
+                            <expand macro="pluspfp_08gb"/>
+                            <expand macro="pluspfp_16gb"/>
+                        </param>
+                    </when>
+                </conditional>
+            </when>
+            <when value="special_prebuilt">
+                <conditional name="special_prebuild">
+                    <param name="special_prebuilt_db" type="select" multiple="false" label="Select pre-built database to download">
+                        <option value="eupathdb48_20230407">EuPathDB-46 (April 7, 2023)</option>
+                        <option value="eupathdb48_20201113">EuPathDB-46 (November 13, 2020)</option>
+                    </param>
+                    <when value="eupathdb48_20230407">
+                        <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
+                        <param name="prebuilt_date" type="hidden" value="2023-04-07"/>
+                    </when>
+                    <when value="eupathdb48_20201113">
+                        <param name="prebuilt_db" type="hidden" value="eupathdb48"/>
+                        <param name="prebuilt_date" type="hidden" value="2020-11-13"/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="minikraken">
+                <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download">
+                    <option value="v2">Version 2</option>
+                    <option value="v1">Version 1</option>
+                </param>
+            </when>
+            <when value="special">
+                <param name="special_database_type" type="select" multiple="false" label="Select database to build">
+                    <option value="greengenes">Greengenes</option>
+                    <option value="silva">Silva</option>
+                    <option value="rdp">RDP</option>
+                </param>
+                <expand macro="common_params" />
+            </when>
+            <when value="custom">
+                <param name="custom_fasta" type="data" format="fasta" multiple="False" label="Select history item" />
+                <param name="custom_database_name" type="text" label="Name for this database" />
+                <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" />
+                <param name="skip_maps" type="boolean" truevalue="--skip-maps" falsevalue="" label="Skip downloading accession number to taxid maps during taxonomy download." />
+                <expand macro="common_params" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <conditional name="database_type">
+                <param name="database_type" value="custom" />
+                <param name="custom_fasta" value="adapter.fa" />
+                <param name="custom_database_name" value="custom_database" />
+                <param name="custom_source_info" value="from adapter.fa test data" />
+                <param name="skip_maps" value="true" />
+                <param name="kmer_len" value="35" />
+                <param name="minimizer_spaces" value="6"/>
+                <param name="load_factor" value="0.7" />
+                <param name="clean" value="true"/>
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="kraken2_databases"/>
+                    <has_text text="path"/>
+                    <has_text text="custom_database (from adapter.fa test data, kmer-len=35, minimizer-len=31, minimizer-spaces=6, load-factor=0.7)"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <conditional name="database_type">
+                <param name="database_type" value="standard_prebuilt" />
+                <conditional name="prebuild">
+                    <param name="prebuilt_date" value="2022-06-07"/>
+                    <param name="prebuilt_db" value="viral"/>
+                </conditional>
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="kraken2_databases"/>
+                    <has_text text="path"/>
+                    <has_text text="Viral"/>
+                    <has_text text="_standard_prebuilt_viral_2022-06-07"/>
+                    <has_text text="Version"/>
+                    <has_text text="Downloaded"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test with latest version -->
+        <test>
+            <conditional name="database_type">
+                <param name="database_type" value="standard_prebuilt" />
+                <conditional name="prebuild">
+                    <param name="prebuilt_date" value="2024-01-12"/>
+                    <param name="prebuilt_db" value="viral"/>
+                </conditional>
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="kraken2_databases"/>
+                    <has_text text="path"/>
+                    <has_text text="Viral"/>
+                    <has_text text="_standard_prebuilt_viral_2024-01-12"/>
+                    <has_text text="Version"/>
+                    <has_text text="Downloaded"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- test with first 2024 version -->
+        <test>
+            <conditional name="database_type">
+                <param name="database_type" value="standard_prebuilt" />
+                <conditional name="prebuild">
+                    <param name="prebuilt_date" value="2024-06-05"/>
+                    <param name="prebuilt_db" value="viral"/>
+                </conditional>
+            </conditional>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="kraken2_databases"/>
+                    <has_text text="path"/>
+                    <has_text text="Viral"/>
+                    <has_text text="_standard_prebuilt_viral_2024-06-05"/>
+                    <has_text text="Version"/>
+                    <has_text text="Downloaded"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+Build Kraken2 databases or download `prebuilt Kraken2 RefSeq indexes <https://benlangmead.github.io/aws-indexes/k2>`__
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1186/s13059-019-1891-0</citation>
+    </citations>
+</tool>