# HG changeset patch # User peterjc # Date 1437555538 14400 # Node ID 188d2aca045bb1f8c2e2260bfb620548a496d78e # Parent a679e0072009fff32f3e9e698af3071ce4bdc21b Uploaded v0.1.04, fix regression with BLAST database from history diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/README.rst Wed Jul 22 04:58:58 2015 -0400 @@ -215,6 +215,9 @@ - Added "NCBI BLAST+ integrated into Galaxy" preprint citation. v0.1.03 - Reorder XML elements (internal change only). - Planemo for Tool Shed upload (``.shed.yml``, internal change only). +v0.1.04 - Fixed regression using BLAST databases from the history. Currently + Galaxy inputs must still use ``.extra_files_path`` rather than the + more consise ``.extra_files`` available for output files (Issue #69) ======= ====================================================================== diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Show BLAST database information from blastdbcmd blastdbcmd diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Extract sequence(s) from BLAST database blastdbcmd diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Search nucleotide database with nucleotide query sequence(s) diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Search protein database with protein query sequence(s) diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Search protein database with translated nucleotide query sequence(s) diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb convert2blastmask diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + masks low complexity regions diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Wed Jul 22 04:58:58 2015 -0400 @@ -349,7 +349,7 @@ #if $db_opts.db_opts_selector == "db": -db "${db_opts.database.fields.path}" #elif $db_opts.db_opts_selector == "histdb": - -db "${os.path.join($db_opts.histdb.files_path,'blastdb')}" + -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}" #else: -subject "$db_opts.subject" #end if diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Make BLAST database makeblastdb diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Make profile database makeprofiledb diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Search protein domain database (PSSMs) with protein query sequence(s) diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Search protein domain database (PSSMs) with translated nucleotide query sequence(s) diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + low-complexity regions in protein sequences segmasker diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Search translated nucleotide database with protein query sequence(s) diff -r a679e0072009 -r 188d2aca045b tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Sun Jul 05 10:36:30 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Jul 22 04:58:58 2015 -0400 @@ -1,4 +1,4 @@ - + Search translated nucleotide database with translated nucleotide query sequence(s)