| Previous changeset 2:a6a81f921701 (2020-03-29) Next changeset 4:38ccd4589990 (2020-11-22) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit 8533fe71d1d50f09348da2dc34941724407a1ffe" |
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modified:
data_manager/dada2_fetcher.xml data_manager/data_manager.py |
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| diff -r a6a81f921701 -r c29275496061 data_manager/dada2_fetcher.xml --- a/data_manager/dada2_fetcher.xml Sun Mar 29 17:51:21 2020 -0400 +++ b/data_manager/dada2_fetcher.xml Tue Jul 14 07:37:09 2020 -0400 |
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| @@ -1,9 +1,9 @@ <?xml version="1.0"?> -<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" profile="18.09" version="0.0.9"> - <description>Download reference databases</description> +<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" version="0.0.7"> <requirements> <requirement type="package" version="3.7">python</requirement> </requirements> + <description>Download reference databases</description> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/data_manager.py' --out '$out_file' @@ -27,7 +27,6 @@ </param> <when value="silva"> <param name="version_select" type="select" label="Database version"> - <option value="138">138</option> <option value="132">132</option> <option value="128">128</option> </param> @@ -82,11 +81,6 @@ <tests> <test> <param name="db_cond|db_select" value="silva"/> - <param name="db_cond|version_select" value="138"/> - <output name="out_file" file="silva138_json"/> - </test> - <test> - <param name="db_cond|db_select" value="silva"/> <param name="db_cond|version_select" value="132"/> <output name="out_file" file="silva132_json"/> </test> |
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| diff -r a6a81f921701 -r c29275496061 data_manager/data_manager.py --- a/data_manager/data_manager.py Sun Mar 29 17:51:21 2020 -0400 +++ b/data_manager/data_manager.py Tue Jul 14 07:37:09 2020 -0400 |
| [ |
| @@ -105,7 +105,7 @@ workdir = params['output_data'][0]['extra_files_path'] os.mkdir(workdir) - url_download( FILE2TAXURL[dataset], dataset + ".taxonomy", workdir) + url_download(FILE2TAXURL[dataset], dataset + ".taxonomy", workdir) data_manager_json = {"data_tables": {}} data_manager_entry = {} @@ -115,8 +115,8 @@ data_manager_entry['taxlevels'] = FILE2TAXLEVELS.get(dataset, DEFAULT_TAXLEVELS) data_manager_json["data_tables"]["dada2_taxonomy"] = data_manager_entry - if FILE2SPECIESURL.get(dataset, False ): - url_download( FILE2SPECIESURL[dataset], dataset + ".species", workdir) + if FILE2SPECIESURL.get(dataset, False): + url_download(FILE2SPECIESURL[dataset], dataset + ".species", workdir) data_manager_entry = {} data_manager_entry['value'] = dataset data_manager_entry['name'] = FILE2NAME[dataset] |