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changeset 5:188d2aca045b draft

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Uploaded v0.1.04, fix regression with BLAST database from history
author peterjc
date Wed, 22 Jul 2015 04:58:58 -0400
parents a679e0072009
children 856b73016ba1
files 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
diffstat 16 files changed, 18 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- 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)
 ======= ======================================================================
 
 
--- 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 @@
-<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>
--- 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 @@
-<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>
--- 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 @@
-<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>
--- 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 @@
-<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" />
--- 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 @@
-<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>
--- 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 @@
-<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>
--- 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 @@
-<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>
--- 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
--- 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 @@
-<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>
--- 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 @@
-<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>
--- 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 @@
-<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" />
--- 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 @@
-<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>
--- 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 @@
-<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>
--- 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 @@
-<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>
--- 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 @@
-<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>