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Add new DBs for MAPseq #6379

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merged 7 commits into from
Sep 30, 2024
Merged

Add new DBs for MAPseq #6379

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5d9db30
add new DBs
RZ9082 Sep 27, 2024
7981599
flake8
RZ9082 Sep 27, 2024
dcd584f
Update mapseq_db_fetcher.xml
bgruening Sep 27, 2024
ff2e253
Merge branch 'galaxyproject:main' into mapseq-datamanager
RZ9082 Sep 30, 2024
91db4c4
update test
RZ9082 Sep 30, 2024
414458a
add test files
RZ9082 Sep 30, 2024
f5b416a
fix indentation
RZ9082 Sep 30, 2024
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26 changes: 18 additions & 8 deletions data_managers/data_manager_mapseq/data_manager/data_manager_fetch_mapseq_db.py
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Expand Up @@ -10,18 +10,28 @@
import wget

DB_paths = {
"mgnify_lsu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_lsu-20200130.tar.gz",
"mgnify_ssu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_ssu-20200130.tar.gz",
"mgnify_its_unite": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/UNITE-20200214.tar.gz",
"mgnify_its_itsonedb": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/ITSoneDB-20200214.tar.gz",
"mgnify_v5_lsu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_lsu-20200130.tar.gz",
"mgnify_v5_ssu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/silva_ssu-20200130.tar.gz",
"mgnify_v5_its_unite": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/UNITE-20200214.tar.gz",
"mgnify_v5_its_itsonedb": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipeline-5.0/ref-dbs/ITSoneDB-20200214.tar.gz",
"mgnify_v6_lsu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/silva-lsu/silva-lsu_138.1.tar.gz",
"mgnify_v6_ssu": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/silva-ssu/silva-ssu_138.1.tar.gz",
"mgnify_v6_its_unite": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/unite/unite_9.0.tar.gz",
"mgnify_v6_its_itsonedb": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/itsonedb/itsonedb_1.141.tar.gz",
"mgnify_v6_pr2": "ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/pipelines/tool-dbs/pr2/pr2_5.0.0.tar.gz",
"test_lsu": "https://zenodo.org/record/8205348/files/test_lsu.tar.gz",
}

DB_names = {
"mgnify_lsu": "MGnify LSU (v5.0.7) - silva_lsu-20200130",
"mgnify_ssu": "MGnify SSU (v5.0.7) - silva_ssu-20200130",
"mgnify_its_unite": "MGnify ITS UNITE (v5.0.7) - UNITE-20200214",
"mgnify_its_itsonedb": "MGnify ITS ITSonedb (v5.0.7) - ITSoneDB-20200214",
"mgnify_v5_lsu": "MGnify LSU (v5.0.7) - silva_lsu-20200130",
"mgnify_v5_ssu": "MGnify SSU (v5.0.7) - silva_ssu-20200130",
"mgnify_v5_its_unite": "MGnify ITS UNITE (v5.0.7) - UNITE-20200214",
"mgnify_v5_its_itsonedb": "MGnify ITS ITSonedb (v5.0.7) - ITSoneDB-20200214",
"mgnify_v6_lsu": "MGnify LSU (v6.0) - silva_lsu-20240702",
"mgnify_v6_ssu": "MGnify SSU (v6.0) - silva_ssu-20240701",
"mgnify_v6_its_unite": "MGnify ITS UNITE (v6.0) - UNITE-20240702",
"mgnify_v6_its_itsonedb": "MGnify ITS ITSonedb (v6.0) - ITSoneDB-20240702",
"mgnify_v6_pr2": "MGnify PR2 (v6.0) - PR2-20240702",
"test_lsu": "Trimmed LSU Test DB",
}

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2 changes: 1 addition & 1 deletion data_managers/data_manager_mapseq/data_manager/macros.xml
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@@ -1,7 +1,7 @@
<?xml version="1.0"?>
<macros>
<token name="@TOOL_VERSION@">1.1</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@PROFILE@">22.05</token>
<xml name="requirements">
<requirements>
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32 changes: 18 additions & 14 deletions data_managers/data_manager_mapseq/data_manager/mapseq_db_fetcher.xml
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@@ -1,4 +1,3 @@
<?xml version="1.0"?>
<tool id="mapseq_db_fetcher" name="Mapseq DB fetcher" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>Fetches the DB required for mapseq</description>
<macros>
Expand All @@ -16,18 +15,23 @@
]]>
</command>
<inputs>
<!-- <param name="test_data_manager" type="hidden" /> -->
<param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." />

<param name="database_type" type="select" multiple="false" label="Database Type">
<option value="mgnify_lsu">MGnify LSU (v5.0.7)</option>
<option value="mgnify_ssu">MGnify SSU (v5.0.7)</option>
<option value="mgnify_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
<option value="mgnify_its_unite">MGnify ITS UNITE (v5.0.7)</option>
</param>

<!-- <param name="test_data_manager" type="text" value=""/> -->
<param argument="--version" type="text" value="5.0.7" help="Check MGnify GitHub (https://github.com/EBI-Metagenomics/pipeline-v5/releases) for the version."/>
<!-- <param name="test_data_manager" type="hidden" /> -->
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<param name="test_data_manager" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." />

<param name="database_type" type="select" multiple="false" label="Database Type">
<option value="mgnify_v6_lsu">MGnify LSU (v6.0)</option>
<option value="mgnify_v6_ssu">MGnify SSU (v6.0)</option>
<option value="mgnify_v6_its_itsonedb">MGnify ITS ITSonedb (v6.0)</option>
<option value="mgnify_v6_its_unite">MGnify ITS UNITE (v6.0)</option>
<option value="mgnify_v6_pr2">MGnify PR2 (v6.0)</option>
<option value="mgnify_v5_lsu">MGnify LSU (v5.0.7)</option>
<option value="mgnify_v5_ssu">MGnify SSU (v5.0.7)</option>
<option value="mgnify_v5_its_itsonedb">MGnify ITS ITSonedb (v5.0.7)</option>
<option value="mgnify_v5_its_unite">MGnify ITS UNITE (v5.0.7)</option>
</param>

<!-- <param name="test_data_manager" type="text" value=""/> -->
<param argument="--version" type="text" value="6.0" help="Check MGnify GitHub (https://github.com/EBI-Metagenomics/amplicon-pipeline) for the version."/>
</inputs>
<outputs>
<data format="data_manager_json" name="out_file" />
Expand All @@ -51,4 +55,4 @@
</help>
<expand macro="citations" />
<expand macro="creator" />
</tool>
</tool>
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