Mercurial > repos > jjohnson > eggnog_mapper
changeset 4:ea9772670fb5 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit ab8f3af4dd052475db01f8120df0f9da6e8fff29
| author | jjohnson |
|---|---|
| date | Wed, 06 Nov 2019 14:06:45 -0500 |
| parents | 9d94fe7ce8b9 |
| children | a093b9061498 |
| files | data_manager/data_manager_eggnog.py data_manager/data_manager_eggnog.xml |
| diffstat | 2 files changed, 12 insertions(+), 6 deletions(-) [+] |
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--- a/data_manager/data_manager_eggnog.py Tue Nov 05 15:53:42 2019 -0500 +++ b/data_manager/data_manager_eggnog.py Wed Nov 06 14:06:45 2019 -0500 @@ -44,7 +44,7 @@ dm_dict['data_tables'][data_table]\ = dm_dict['data_tables'].get(data_table, []) data_table_entry = dict(value=db_version, name=db_version, - path=eggnog_db_path) + path=args.install_path) dm_dict['data_tables'][data_table].append(data_table_entry) data_table = 'eggnog_mapper_hmm_dbs' dm_dict['data_tables'][data_table]\
--- a/data_manager/data_manager_eggnog.xml Tue Nov 05 15:53:42 2019 -0500 +++ b/data_manager/data_manager_eggnog.xml Wed Nov 06 14:06:45 2019 -0500 @@ -16,14 +16,19 @@ #else #set $eggnogdbs = 'none' #end if -#if $test == 'false' +#if $test == 'true' +#import os.path +#set $install_path = $os.path.join($os.path.dirname($__tool_directory__), 'test-data/cached_locally') +echo $install_path >> /Users/jj/gxt/gxt/eggnog_install_path && +#end if mkdir -p '${install_path}' && download_eggnog_data.py - $diamond_database -y -q --data_dir $install_path $eggnogdbs -' '.join(dbs.split(',')) && -#else -#set $install_path = '/Users/jj/gx/gh/jj/tools-galaxyp/tools/eggnog_mapper/test-data/cached_locally' + $diamond_database -y -q +#if $test == 'true' + -s #end if + --data_dir '$install_path' + $eggnogdbs && python '${__tool_directory__}/data_manager_eggnog.py' --config_file '$out_file' --install_path '$install_path' --dbs '$dbs' ]]></command> <inputs> @@ -150,6 +155,7 @@ <test> <param name="test" value="true"/> <param name="diamond_database" value="false"/> + <param name="dbs" value="thaNOG"/> <output name="out_file"> <assert_contents> <has_text text="eggnog_mapper_db" />