| Previous changeset 1:4cd97cc67061 (2024-03-23) Next changeset 3:a0d77af1d226 (2024-12-03) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit 960c1f69ec78943dfe72eff0a0992a2ce15d2555 |
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modified:
data_manager_fetch_mapseq_db.py macros.xml mapseq_db_fetcher.xml |
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| diff -r 4cd97cc67061 -r 23511530b8fd data_manager_fetch_mapseq_db.py --- a/data_manager_fetch_mapseq_db.py Sat Mar 23 07:20:14 2024 +0000 +++ b/data_manager_fetch_mapseq_db.py Mon Sep 30 10:08:03 2024 +0000 |
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| @@ -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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| diff -r 4cd97cc67061 -r 23511530b8fd macros.xml --- a/macros.xml Sat Mar 23 07:20:14 2024 +0000 +++ b/macros.xml Mon Sep 30 10:08:03 2024 +0000 |
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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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| diff -r 4cd97cc67061 -r 23511530b8fd mapseq_db_fetcher.xml --- a/mapseq_db_fetcher.xml Sat Mar 23 07:20:14 2024 +0000 +++ b/mapseq_db_fetcher.xml Mon Sep 30 10:08:03 2024 +0000 |
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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> @@ -12,36 +11,54 @@ --out '${out_file}' --version '${version}' --database-type '${database_type}' - $test_data_manager + $test_data_manager_v5 + $test_data_manager_v6 ]]> </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" /> --> + <param name="test_data_manager_v5" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry." /> + <param name="test_data_manager_v6" 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" /> </outputs> <tests> <test expect_num_outputs="1"> - <param name="test_data_manager" value="--test"/> + <param name="test_data_manager_v5" value="--test"/> <param name="version" value="5.0.7"/> - <param name="database_type" value="mgnify_lsu"/> + <param name="database_type" value="mgnify_v5_lsu"/> <output name="out_file"> - <assert_contents> - <has_text text="mgnify_lsu"/> - <has_text text="5.0.7"/> - </assert_contents> + <assert_contents> + <has_text text="mgnify_v5_lsu"/> + <has_text text="5.0.7"/> + </assert_contents> + </output> + </test> + <test expect_num_outputs="1"> + <param name="test_data_manager_v6" value="--test"/> + <param name="version" value="6.0"/> + <param name="database_type" value="mgnify_v6_pr2"/> + <output name="out_file"> + <assert_contents> + <has_text text="mgnify_v6_pr2"/> + <has_text text="6.0"/> + </assert_contents> </output> </test> </tests> @@ -51,4 +68,4 @@ </help> <expand macro="citations" /> <expand macro="creator" /> -</tool> \ No newline at end of file +</tool> |