Mercurial > repos > devteam > kraken
changeset 1:656215d2a793 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit cb1743eafd4ca98be0148d557770ef8635cc8d4c-dirty
| author | devteam |
|---|---|
| date | Tue, 19 May 2015 16:41:06 -0400 |
| parents | 7d6b55e6417e |
| children | 898ded2d4fff |
| files | kraken.xml macros.xml tool_dependencies.xml |
| diffstat | 3 files changed, 4 insertions(+), 2 deletions(-) [+] |
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--- a/kraken.xml Wed Apr 22 13:03:24 2015 -0400 +++ b/kraken.xml Tue May 19 16:41:06 2015 -0400 @@ -8,6 +8,7 @@ </macros> <command> <![CDATA[ + @SET_DATABASE_PATH@ && kraken --threads \${GALAXY_SLOTS:-1} @INPUT_DATABASE@ "$input_sequences" #if $split_reads:
--- a/macros.xml Wed Apr 22 13:03:24 2015 -0400 +++ b/macros.xml Tue May 19 16:41:06 2015 -0400 @@ -25,5 +25,6 @@ <citation type="doi">10.1186/gb-2014-15-3-r46</citation> </citations> </xml> - <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.path}/${kraken_database.fields.name}</token> + <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token> + <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token> </macros> \ No newline at end of file
--- a/tool_dependencies.xml Wed Apr 22 13:03:24 2015 -0400 +++ b/tool_dependencies.xml Tue May 19 16:41:06 2015 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="kraken" version="0.10.5"> - <repository changeset_revision="c949a8bd92ec" name="package_kraken_0_10_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e79fee8f87fa" name="package_kraken_0_10_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>