| Previous changeset 1:bf7b2c14cabc (2019-12-05) Next changeset 3:c29275496061 (2020-07-14) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_dada2 commit a096d3eb593edee6cb08247be3a09138d088a6ce" |
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modified:
data_manager/dada2_fetcher.xml data_manager/data_manager.py |
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added:
test-data/silva138_json |
| b |
| diff -r bf7b2c14cabc -r a6a81f921701 data_manager/dada2_fetcher.xml --- a/data_manager/dada2_fetcher.xml Thu Dec 05 17:58:52 2019 -0500 +++ b/data_manager/dada2_fetcher.xml Sun Mar 29 17:51:21 2020 -0400 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" profile="18.09" version="0.0.8"> +<tool id="dada2_fetcher" name="dada2 data manager" tool_type="manage_data" profile="18.09" version="0.0.9"> <description>Download reference databases</description> <requirements> <requirement type="package" version="3.7">python</requirement> @@ -27,6 +27,7 @@ </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> @@ -81,6 +82,11 @@ <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 bf7b2c14cabc -r a6a81f921701 data_manager/data_manager.py --- a/data_manager/data_manager.py Thu Dec 05 17:58:52 2019 -0500 +++ b/data_manager/data_manager.py Sun Mar 29 17:51:21 2020 -0400 |
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| @@ -11,6 +11,7 @@ DEFAULT_TAXLEVELS = "Kingdom,Phylum,Class,Order,Family,Genus,Species" FILE2NAME = { + "silva_138": "Silva version 138", "silva_132": "Silva version 132", "silva_128": "Silva version 128", "rdp_16": "RDP trainset 16", @@ -26,6 +27,7 @@ } FILE2TAXURL = { + "silva_138": "https://zenodo.org/record/3731176/files/silva_nr_v138_train_set.fa.gz?download=1", "silva_132": "https://zenodo.org/record/1172783/files/silva_nr_v132_train_set.fa.gz?download=1", "silva_128": "https://zenodo.org/record/824551/files/silva_nr_v128_train_set.fa.gz?download=1", "rdp_16": "https://zenodo.org/record/801828/files/rdp_train_set_16.fa.gz?download=1", @@ -41,6 +43,7 @@ } FILE2SPECIESURL = { + "silva_138": "https://zenodo.org/record/3731176/files/silva_species_assignment_v138.fa.gz?download=1", "silva_132": "https://zenodo.org/record/1172783/files/silva_species_assignment_v132.fa.gz?download=1", "silva_128": "https://zenodo.org/record/824551/files/silva_species_assignment_v128.fa.gz?download=1", "rdp_16": "https://zenodo.org/record/801828/files/rdp_species_assignment_16.fa.gz?download=1", |
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| diff -r bf7b2c14cabc -r a6a81f921701 test-data/silva138_json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/silva138_json Sun Mar 29 17:51:21 2020 -0400 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"dada2_species": {"name": "Silva version 138", "path": "silva_138.species", "value": "silva_138"}, "dada2_taxonomy": {"name": "Silva version 138", "path": "silva_138.taxonomy", "taxlevels": "Kingdom,Phylum,Class,Order,Family,Genus,Species", "value": "silva_138"}}} \ No newline at end of file |