| Previous changeset 1:1ff9996995ee (2020-11-22) Next changeset 3:14785f8a3725 (2023-04-16) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mitos commit 2db6284f6077d80d05227180a809b921b4975c60" |
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modified:
data_manager/data_manager.py data_manager/data_manager_mitos.xml |
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added:
test-data/mitos2_refseq63.json |
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| diff -r 1ff9996995ee -r 19d9be08560c data_manager/data_manager.py --- a/data_manager/data_manager.py Sun Nov 22 12:51:27 2020 +0000 +++ b/data_manager/data_manager.py Sun Nov 22 18:03:14 2020 +0000 |
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| @@ -12,7 +12,7 @@ ZENODO = { "mitos": "2683856", - "mitos2": "3685310" + "mitos2": "4284483" } NAMES = { "mitos1-refdata": "RefSeq39 + MiTFi tRNA models", |
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| diff -r 1ff9996995ee -r 19d9be08560c data_manager/data_manager_mitos.xml --- a/data_manager/data_manager_mitos.xml Sun Nov 22 12:51:27 2020 +0000 +++ b/data_manager/data_manager_mitos.xml Sun Nov 22 18:03:14 2020 +0000 |
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| @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.1"> +<tool id="data_manager_mitos" name="MITOS" tool_type="manage_data" version="0.0.2"> <description>reference data downloader</description> <requirements> <requirement type="package" version="3.7">python</requirement> @@ -25,13 +25,13 @@ </when> <when value="mitos2"> <param name="database" type="select" label="Reference data version"> - <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option> <option value="refseq63m">RefSeq63 Metazoa</option> <option value="refseq63f">RefSeq63 Fungi</option> <option value="refseq63o">RefSeq63 Opisthokonta</option> <option value="refseq89m">RefSeq89 Metazoa</option> <option value="refseq89f">RefSeq89 Fungi</option> <option value="refseq89o">RefSeq89 Opisthokonta</option> + <option value="refseq39">RefSeq39 (equivalent to MITOS1 data)</option> </param> </when> </conditional> @@ -47,6 +47,13 @@ </conditional> <output name="out_file" file="mitos_refseq39.json"/> </test> + <test> + <conditional name="type_cond"> + <param name="type_select" value="mitos2"/> + <param name="database" value="refseq63m"/> + </conditional> + <output name="out_file" file="mitos2_refseq63.json"/> + </test> </tests> <help> This data manager downloads MITOS and MITOS2 reference data for use in Galaxy. @@ -74,7 +81,7 @@ - covariance models computed for the data in the RefSeq releas based on the MITOS1 models - in addition for Metazoa Release 63 also hidden markov models are available as described in Al Arab et al. 2017 -Data is downloaded from https://zenodo.org/record/3685310. +Data is downloaded from https://zenodo.org/record/4284483. </help> <citations> <citation type="doi">10.1016/j.ympev.2012.08.023</citation> |
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| diff -r 1ff9996995ee -r 19d9be08560c test-data/mitos2_refseq63.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos2_refseq63.json Sun Nov 22 18:03:14 2020 +0000 |
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| @@ -0,0 +1,1 @@ +{"data_tables": {"mitos": {"name": "RefSeq63 Metazoa", "path": "refseq63m", "type": "mitos2", "value": "refseq63m"}}} \ No newline at end of file |