# HG changeset patch # User peterjc # Date 1599661973 0 # Node ID 1ebae91eb6e9770102156f9da506a9ea3fc06215 # Parent 8146c9884047d76b67dd92c7d40ca3bdc2660905 "planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit 0c82b9ef284c686cbffd30582d2586e4fb52881e-dirty" diff -r 8146c9884047 -r 1ebae91eb6e9 tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Wed Sep 09 13:12:55 2020 +0000 +++ b/tools/ncbi_blast_plus/README.rst Wed Sep 09 14:32:53 2020 +0000 @@ -141,7 +141,9 @@ ``tool_dependencies.xml`` files. Instead assumes conda for dependency resolution and requires at least Galaxy v16.10 which includes the BLAST datatypes. - - ``blastdbcmd`` wrapper supports multiple databases + - ``blastdbcmd`` wrapper supports multiple locally installed + databases (contribution from Frederic Sapet), or a database + from your Galaxy history. ============== =============================================================== Prior releases used a self-contained version number (deliberately kept low to diff -r 8146c9884047 -r 1ebae91eb6e9 tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Sep 09 13:12:55 2020 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Sep 09 14:32:53 2020 +0000 @@ -6,33 +6,35 @@ -blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path.replace(',',' ')}" -info -out "$info" +blastdbcmd +@DBCMD_OPTS@ +-info -out "$info" - + - + - + - + - + diff -r 8146c9884047 -r 1ebae91eb6e9 tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Sep 09 13:12:55 2020 +0000 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Sep 09 14:32:53 2020 +0000 @@ -8,7 +8,8 @@ ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces -blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path.replace(',',' ')}" +blastdbcmd +@DBCMD_OPTS@ ##TODO: What about -ctrl_a and -target_only as advanced options? @@ -67,12 +68,15 @@ - + + + - + + @@ -81,7 +85,7 @@ - + @@ -90,7 +94,7 @@ - + @@ -98,7 +102,7 @@ - + @@ -107,7 +111,7 @@ - + diff -r 8146c9884047 -r 1ebae91eb6e9 tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Wed Sep 09 13:12:55 2020 +0000 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Wed Sep 09 14:32:53 2020 +0000 @@ -428,14 +428,40 @@ - - - + + + + + + + + + + + + + + + + - - - + + + + + + + + + + + + + + + + @@ -576,6 +602,17 @@ #end if ]]> + + + + + + +