Mercurial > repos > bgruening > pg_query
diff macros.xml @ 0:fa1a61331039 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tools/pgtools commit ab93c4c70fa487e55a24863a7786e102e7d92272
author | bgruening |
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date | Wed, 24 Apr 2019 06:12:05 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 24 06:12:05 2019 -0400 @@ -0,0 +1,76 @@ +<?xml version="1.0"?> +<macros> + <xml name="inputs_outputs"> + <inputs> + <param format="tabular" help="" label="Input tabular dataset" name="in_file" type="data" /> + <yield /> + </inputs> + <outputs> + <data format="tabular" name="out_file" label="${tool.name} on ${on_string}" /> + </outputs> + </xml> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="@PG_VERSION@">postgresql</requirement> + <requirement type="package" version="0.1">pglite</requirement> + </requirements> + </xml> + + <token name="@PG_VERSION@">11.2</token> + + <token name="@HELP_FOOTER@"> + The postgresql tools, are using a postgresql database in user-space. Databases are packed into a tarball and stored in the user-history. + </token> + + <token name="@UNTAR_INFILE@"><![CDATA[ + tar -xjvf '$infile' && + export PWD=`pwd` && + sed -i.bak "s|unix_socket_directories.*|unix_socket_directories = '\$PWD/postgresql/'|" ./postgresql/db/postgresql.conf + ]]> + </token> + + <token name="@PG_SETUP@"><![CDATA[ + pglite setup -d ./postgresql && + @PG_START@ + ]]> + </token> + + <token name="@PSQL@"><![CDATA[ + psql "\$(pglite url -d ./postgresql)" + ]]> + </token> + + <token name="@STATUS_RUNNING@"><![CDATA[ + timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "server is running"; do sleep 1; done' && + pglite status -d ./postgresql && + timeout 60 bash -c 'until ls -la ./postgresql | grep -F -q ".s.PGSQL.5432"; do sleep 1; done' + && pglite status -d ./postgresql + ]]> + </token> + + <token name="@STOPPED@"><![CDATA[ + timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' + ]]> + </token> + + <token name="@PG_START@"><![CDATA[ + pglite start -d ./postgresql && + @STATUS_RUNNING@ + ]]> + </token> + + <token name="@PG_STOP@"><![CDATA[ + pglite stop -d ./postgresql && + @STOPPED@ + ]]> + </token> + + <token name="@ARCHIVE_DATABASE@"><![CDATA[ + tar -cvjf postgresql_out.tar.bz2 postgresql + ]]> + </token> + <xml name="citations"> + <citations></citations> + </xml> +</macros>