1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/12cb939a8147/ changeset: 12cb939a8147 user: kanwei date: 2011-07-12 23:04:16 summary: Rename version_string -> version_command, update wrappers affected #: 7 files (31 bytes) --- a/lib/galaxy/tools/__init__.py Thu Jul 07 11:19:33 2011 +0100 +++ b/lib/galaxy/tools/__init__.py Tue Jul 12 17:04:16 2011 -0400 @@ -397,8 +397,9 @@ self.description = util.xml_text(root, "description") # Versioning for tools self.version_string_cmd = None - if root.find("version_string") is not None: - self.version_string_cmd = root.find("version_string").text + version_cmd = root.find("version_command") + if version_cmd is not None: + self.version_string_cmd = version_cmd.text # Parallelism for tasks, read from tool config. parallelism = root.find("parallelism") if parallelism is not None and parallelism.get("method"): --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.11"><description>Search nucleotide database with nucleotide query sequence(s)</description> - <version_string>blastn -version</version_string> + <version_command>blastn -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11"><description>Search protein database with protein query sequence(s)</description> - <version_string>blastp -version</version_string> + <version_command>blastp -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.11"><description>Search protein database with translated nucleotide query sequence(s)</description> - <version_string>blastx -version</version_string> + <version_command>blastx -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11"><description>Search translated nucleotide database with protein query sequence(s)</description> - <version_string>tblastn -version</version_string> + <version_command>tblastn -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.11"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> - <version_string>tblastx -version</version_string> + <version_command>tblastx -version</version_command><command interpreter="python">hide_stderr.py ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces --- a/tools/ngs_rna/tophat_wrapper.xml Thu Jul 07 11:19:33 2011 +0100 +++ b/tools/ngs_rna/tophat_wrapper.xml Tue Jul 12 17:04:16 2011 -0400 @@ -1,6 +1,6 @@ <tool id="tophat" name="Tophat for Illumina" version="1.5.0"><description>Find splice junctions using RNA-seq data</description> - <version_string>tophat --version</version_string> + <version_command>tophat --version</version_command><requirements><requirement type="package">tophat</requirement></requirements> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.