Mercurial > repos > iuc > data_manager_mapseq
changeset 4:19ef193d1316 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/ commit abbc840d4383eee1f26abef04b1ce4df1e6e20a2
| author | iuc |
|---|---|
| date | Fri, 06 Dec 2024 15:43:18 +0000 |
| parents | a0d77af1d226 |
| children | |
| files | macros.xml mapseq_db_fetcher.xml |
| diffstat | 2 files changed, 25 insertions(+), 30 deletions(-) [+] |
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--- a/macros.xml Tue Dec 03 16:30:34 2024 +0000 +++ b/macros.xml Fri Dec 06 15:43:18 2024 +0000 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">22.05</token> <xml name="requirements"> <requirements>
--- a/mapseq_db_fetcher.xml Tue Dec 03 16:30:34 2024 +0000 +++ b/mapseq_db_fetcher.xml Fri Dec 06 15:43:18 2024 +0000 @@ -9,31 +9,37 @@ <![CDATA[ python '$__tool_directory__/data_manager_fetch_mapseq_db.py' --out '${out_file}' - --version '${version}' + --version '${select_version.version}' --database-type '${database_type}' $test_data_manager_v5 - $test_data_manager_v6 ]]> </command> <inputs> <!-- <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 for v5." /> - <param name="test_data_manager_v6" type="boolean" truevalue="--test" falsevalue="" checked="False" label="Download minimal test DB and create mock data table entry for v6." /> - - <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."/> + <conditional name="select_version"> + <param argument="--version" type="select" label="Select MGnify version"> + <option value="5.0">v5.0</option> + <option value="6.0">v6.0</option> + </param> + <when value="5.0"> + <param name="database_type" type="select" multiple="false" label="Database Type"> + <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> + </when> + <when value="6.0"> + <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> + </param> + </when> + </conditional> </inputs> <outputs> <data format="data_manager_json" name="out_file" /> @@ -50,17 +56,6 @@ </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> <help> Downloads preformatted DBs form MGnify that can be used for mapseq.