| Previous changeset 15:c16c30e9ad5b (2015-07-05) Next changeset 17:697f40151eaf (2015-09-04) |
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Commit message:
Uploaded v0.1.04, fix regression with BLAST database from history |
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modified:
tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml tools/ncbi_blast_plus/ncbi_makeprofiledb.xml tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/README.rst Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -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) ======= ====================================================================== |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_info.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.03"> +<tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.1.04"> <description>Show BLAST database information from blastdbcmd</description> <macros> <token name="@BINARY@">blastdbcmd</token> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastdbcmd_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.1.03"> +<tool id="ncbi_blastdbcmd_wrapper" name="NCBI BLAST+ blastdbcmd entry(s)" version="0.1.04"> <description>Extract sequence(s) from BLAST database</description> <macros> <token name="@BINARY@">blastdbcmd</token> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.03"> +<tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.1.04"> <description>Search nucleotide database with nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.03"> +<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.1.04"> <description>Search protein database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.03"> +<tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.1.04"> <description>Search protein database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_convert2blastmask_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="0.1.03"> +<tool id="ncbi_convert2blastmask_wrapper" name="NCBI BLAST+ convert2blastmask" version="0.1.04"> <description>Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb</description> <macros> <token name="@BINARY@">convert2blastmask</token> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.03"> +<tool id="ncbi_dustmasker_wrapper" name="NCBI BLAST+ dustmasker" version="0.1.04"> <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo --> <description>masks low complexity regions</description> <macros> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -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 |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.03"> +<tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.1.04"> <description>Make BLAST database</description> <macros> <token name="@BINARY@">makeblastdb</token> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_makeprofiledb.xml --- a/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_makeprofiledb.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="0.1.03"> +<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="0.1.04"> <description>Make profile database</description> <macros> <token name="@BINARY@">makeprofiledb</token> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpsblast_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.03"> +<tool id="ncbi_rpsblast_wrapper" name="NCBI BLAST+ rpsblast" version="0.1.04"> <description>Search protein domain database (PSSMs) with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1" /> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.1.03"> +<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.1.04"> <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_segmasker_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.03"> +<tool id="ncbi_segmasker_wrapper" name="NCBI BLAST+ segmasker" version="0.1.04"> <description>low-complexity regions in protein sequences</description> <macros> <token name="@BINARY@">segmasker</token> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.1.03"> +<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.1.04"> <description>Search translated nucleotide database with protein query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> |
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| diff -r c16c30e9ad5b -r b5f1f599d1fb tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Sun Jul 05 10:37:27 2015 -0400 +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml Wed Jul 22 05:01:11 2015 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.1.03"> +<tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.1.04"> <description>Search translated nucleotide database with translated nucleotide query sequence(s)</description> <!-- If job splitting is enabled, break up the query file into parts --> <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" merge_outputs="output1"></parallelism> |