1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b05591d4a963/ Changeset: b05591d4a963 User: dan Date: 2014-09-02 19:15:17 Summary: Quote commandline arguments for extract genomic DNA tool. Affected #: 1 file diff -r 38f8adbf6a47aa05b64c8dd46ee828c36628df31 -r b05591d4a9631cb3d62a95e98153edc4c67ab395 tools/extract/extract_genomic_dna.xml --- a/tools/extract/extract_genomic_dna.xml +++ b/tools/extract/extract_genomic_dna.xml @@ -1,7 +1,7 @@ <tool id="Extract genomic DNA 1" name="Extract Genomic DNA" version="2.2.3"><description>using coordinates from assembled/unassembled genomes</description><command interpreter="python"> - extract_genomic_dna.py $input $out_file1 -o $out_format -d $dbkey + extract_genomic_dna.py "${input}" "${out_file1}" -o "${out_format}" -d "${dbkey}" #if str( $interpret_features ) == "yes": -I @@ -9,17 +9,17 @@ ## Columns to use in input file. #if isinstance( $input.datatype, $__app__.datatypes_registry.get_datatype_by_extension('gff').__class__): - -1 1,4,5,7 --gff + -1 "1,4,5,7" --gff #else: - -1 ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol} + -1 "${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol},${input.metadata.nameCol}" #end if #if $seq_source.index_source == "cached": ## Genomic data from cache. - -g ${GALAXY_DATA_INDEX_DIR} + -g "${GALAXY_DATA_INDEX_DIR}" #else: ## Genomic data from history. - -F $seq_source.ref_file + -F "${seq_source.ref_file}" #end if </command><inputs> 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.