Mercurial > repos > galaxytrakr > data_manager_mapseq
changeset 2:b2591ceb5ec2 draft
planemo upload commit 960e71a63820069f2022e7b146a0f2118cb47d45
| author | galaxytrakr |
|---|---|
| date | Thu, 26 Mar 2026 20:40:41 +0000 |
| parents | 97634e034eed |
| children | 472239da4582 |
| files | data_manager/data_manager_mapseq.xml data_manager/mapseq_db_fetcher.xml data_manager_conf.xml test-data/.gitkeep tool-data/.gitkeep |
| diffstat | 3 files changed, 53 insertions(+), 53 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/data_manager_mapseq.xml Thu Mar 26 20:40:41 2026 +0000 @@ -0,0 +1,52 @@ +<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> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version" /> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/data_manager_fetch_mapseq_db.py' + --out '${out_file}' + --version '${select_version.version}' + --database-type '${database_type}' + ]]> + </command> + <inputs> + <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" /> + </outputs> + <tests> + </tests> + <help> + Downloads preformatted DBs form MGnify that can be used for mapseq. + The download paths were taken from: https://github.com/EBI-Metagenomics/pipeline-v5/ + </help> + <expand macro="citations" /> + <expand macro="creator" /> +</tool> \ No newline at end of file
--- a/data_manager/mapseq_db_fetcher.xml Thu Mar 26 20:29:18 2026 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ -<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> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> - <expand macro="version" /> - <command detect_errors="exit_code"> - <![CDATA[ - python '$__tool_directory__/data_manager_fetch_mapseq_db.py' - --out '${out_file}' - --version '${select_version.version}' - --database-type '${database_type}' - ]]> - </command> - <inputs> - <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" /> - </outputs> - <tests> - </tests> - <help> - Downloads preformatted DBs form MGnify that can be used for mapseq. - The download paths were taken from: https://github.com/EBI-Metagenomics/pipeline-v5/ - </help> - <expand macro="citations" /> - <expand macro="creator" /> -</tool> \ No newline at end of file
--- a/data_manager_conf.xml Thu Mar 26 20:29:18 2026 +0000 +++ b/data_manager_conf.xml Thu Mar 26 20:40:41 2026 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager/mapseq_db_fetcher.xml" id="data_manager_mapseq"> + <data_manager tool_file="data_manager/data_manager_mapseq.xml" id="data_manager_mapseq"> <data_table name="mapseq_db"> <output> <column name="value" />