changeset 28:ce0b2cad3626 draft

planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus commit ec4fcd918fa8b2af60acc60c0f2d591a1a1d7cd7-dirty

--- a/tools/ncbi_blast_plus/README.rst	Fri Sep 15 11:19:48 2017 -0400
+++ b/tools/ncbi_blast_plus/README.rst	Tue Sep 19 07:41:16 2017 -0400
@@ -248,6 +248,8 @@
           parameter (contribution from Nicola Soranzo).
         - Add ``-max_hsps`` option (contribution from Nicola Soranzo).
         - Add ``-use_sw_tback`` option for BLASTP (Nicola Soranzo).
+v0.2.02 - Document the BLAST+ 2.5.0 change in the standard 12 column output
+          from ``qseqid,sseqid,...`` to ``qacc,sacc,...`` instead.
 ======= ======================================================================
 
 

--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py	Fri Sep 15 11:19:48 2017 -0400
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py	Tue Sep 19 07:41:16 2017 -0400
@@ -108,6 +108,9 @@
 The columns option can be 'std' (standard 12 columns), 'ext'
 (extended 25 columns), or a list of BLAST+ column names like
 'qseqid,sseqid,pident' (space or comma separated).
+
+Note if using a list of column names, currently ONLY the 25
+extended column names are supported.
 """
 parser = OptionParser(usage=usage)
 parser.add_option('-o', '--output', dest='output', default=None,

--- a/tools/ncbi_blast_plus/ncbi_macros.xml	Fri Sep 15 11:19:48 2017 -0400
+++ b/tools/ncbi_blast_plus/ncbi_macros.xml	Tue Sep 19 07:41:16 2017 -0400
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@WRAPPER_VERSION@">0.2.01</token>
+    <token name="@WRAPPER_VERSION@">0.2.02</token>
     <xml name="parallelism">
         <!-- 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" />
@@ -421,8 +421,8 @@
 ====== ========= ============================================
 Column NCBI name Description
 ------ --------- --------------------------------------------
-     1 qseqid    Query Seq-id (ID of your sequence)
-     2 sseqid    Subject Seq-id (ID of the database hit)
+     1 qacc      Query accession
+     2 sacc      Subject accession (database hit)
      3 pident    Percentage of identical matches
      4 length    Alignment length
      5 mismatch  Number of mismatches
@@ -435,6 +435,12 @@
     12 bitscore  Bit score
 ====== ========= ============================================
 
+Until BLAST+ 2.5.0, the first two columns were ``qseqid`` and ``sseqid``,
+which were usually strings contained multiple pipe-separated entries.
+In BLAST+ 2.5.0, the first two columns became ``qacc`` and ``sacc``
+(accesion only), while in BLAST+ 2.6.0 this was changed again to use
+``qaccver`` and ``saccver`` (accession dot version).
+
 The BLAST+ tools can optionally output additional columns of information,
 but this takes longer to calculate. Many commonly used extra columns are
 included by selecting the extended tabular output. The extra columns are