Mercurial > repos > devteam > kraken_translate
diff macros.xml @ 4:9a5be5b1a5c9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 06345505a91f3dcfa8a37dceb6f25e95806dddc8"
| author | iuc |
|---|---|
| date | Wed, 04 Dec 2019 06:51:08 -0500 |
| parents | 9bdcba262627 |
| children | 8cebdc74a48f |
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--- a/macros.xml Mon Aug 07 17:29:45 2017 -0400 +++ b/macros.xml Wed Dec 04 06:51:08 2019 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">1.2.3</token> + <token name="@WRAPPER_VERSION@">1.3.1</token> <xml name="requirements"> <requirements> - <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement> + <requirement type="package" version="1.1.1">kraken</requirement> </requirements> </xml> <xml name="version_command"> @@ -23,6 +23,10 @@ <citation type="doi">10.1186/gb-2014-15-3-r46</citation> </citations> </xml> - <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token> - <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token> + <!-- See the kraken_databases.loc.sample documentation, + this if statement is for backward compatibility as early + versions of the wrapper assumed the UI facing field name + was also part of the directory path --> + <token name="@SET_DATABASE_PATH@">if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi</token> + <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token> </macros>