# HG changeset patch
# User peterjc
# Date 1441615202 14400
# Node ID 75ab3e2cfa0e7925f9fe45cb4ac67543a513935b
# Parent  b41f8c43705e9887a92f7e2aa7996698dd004733
v0.1.8 - Using BLAST+ 2.2.31

diff -r b41f8c43705e -r 75ab3e2cfa0e test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular
--- a/test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular	Fri Sep 04 07:05:56 2015 -0400
+++ b/test-data/rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular	Mon Sep 07 04:40:02 2015 -0400
@@ -1,2 +1,2 @@
 #A_id	B_id	A_length	B_length	A_qcovhsp	B_qcovhsp	length	pident	bitscore
-ENA|BC112106|BC112106.1	gi|57163782|ref|NM_001009242.1|	1213	1047	86	100	1047	92.07	 1514
+ENA|BC112106|BC112106.1	gi|57163782|ref|NM_001009242.1|	1213	1047	86	100	1047	92.07	1514
diff -r b41f8c43705e -r 75ab3e2cfa0e test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular
--- a/test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular	Fri Sep 04 07:05:56 2015 -0400
+++ b/test-data/rbh_blastp_four_human_vs_rhodopsin_proteins.tabular	Mon Sep 07 04:40:02 2015 -0400
@@ -1,2 +1,2 @@
 #A_id	B_id	A_length	B_length	A_qcovhsp	B_qcovhsp	length	pident	bitscore
-sp|P08100|OPSD_HUMAN	gi|57163783|ref|NP_001009242.1|	348	348	100	100	348	96.55	  701
+sp|P08100|OPSD_HUMAN	gi|57163783|ref|NP_001009242.1|	348	348	100	100	348	96.55	701
diff -r b41f8c43705e -r 75ab3e2cfa0e test-data/rbh_blastp_k12.tabular
--- a/test-data/rbh_blastp_k12.tabular	Fri Sep 04 07:05:56 2015 -0400
+++ b/test-data/rbh_blastp_k12.tabular	Mon Sep 07 04:40:02 2015 -0400
@@ -1,10 +1,10 @@
 #A_id	B_id	A_length	B_length	A_qcovhsp	B_qcovhsp	length	pident	bitscore
 gi|16127995|ref|NP_414542.1|	gi|16127995|ref|NP_414542.1|	21	21	100	100	21	100.00	38.1
-gi|16127996|ref|NP_414543.1|	gi|16127996|ref|NP_414543.1|	820	820	100	100	820	100.00	 1687
-gi|16127997|ref|NP_414544.1|	gi|16127997|ref|NP_414544.1|	310	310	100	100	310	100.00	  642
-gi|16127998|ref|NP_414545.1|	gi|16127998|ref|NP_414545.1|	428	428	100	100	428	100.00	  882
-gi|16128000|ref|NP_414547.1|	gi|16128000|ref|NP_414547.1|	258	258	100	100	258	100.00	  531
-gi|16128001|ref|NP_414548.1|	gi|16128001|ref|NP_414548.1|	476	476	100	100	476	100.00	  959
-gi|16128002|ref|NP_414549.1|	gi|16128002|ref|NP_414549.1|	317	317	100	100	317	100.00	  648
-gi|16128003|ref|NP_414550.1|	gi|16128003|ref|NP_414550.1|	195	195	100	100	195	100.00	  397
-gi|16128004|ref|NP_414551.1|	gi|16128004|ref|NP_414551.1|	188	188	100	100	188	100.00	  365
+gi|16127996|ref|NP_414543.1|	gi|16127996|ref|NP_414543.1|	820	820	100	100	820	100.00	1687
+gi|16127997|ref|NP_414544.1|	gi|16127997|ref|NP_414544.1|	310	310	100	100	310	100.00	642
+gi|16127998|ref|NP_414545.1|	gi|16127998|ref|NP_414545.1|	428	428	100	100	428	100.00	882
+gi|16128000|ref|NP_414547.1|	gi|16128000|ref|NP_414547.1|	258	258	100	100	258	100.00	531
+gi|16128001|ref|NP_414548.1|	gi|16128001|ref|NP_414548.1|	476	476	100	100	476	100.00	959
+gi|16128002|ref|NP_414549.1|	gi|16128002|ref|NP_414549.1|	317	317	100	100	317	100.00	648
+gi|16128003|ref|NP_414550.1|	gi|16128003|ref|NP_414550.1|	195	195	100	100	195	100.00	397
+gi|16128004|ref|NP_414551.1|	gi|16128004|ref|NP_414551.1|	188	188	100	100	188	100.00	365
diff -r b41f8c43705e -r 75ab3e2cfa0e test-data/rbh_blastp_k12_self.tabular
--- a/test-data/rbh_blastp_k12_self.tabular	Fri Sep 04 07:05:56 2015 -0400
+++ b/test-data/rbh_blastp_k12_self.tabular	Mon Sep 07 04:40:02 2015 -0400
@@ -1,5 +1,5 @@
 #A_id	B_id	A_length	B_length	A_qcovhsp	B_qcovhsp	length	pident	bitscore
-gi|16127997|ref|NP_414544.1|	NP_414544_near_copy	310	309	99	100	309	99.68	  638
-NP_414544_near_copy	gi|16127997|ref|NP_414544.1|	309	310	100	99	309	99.68	  638
-NP_414546_near_copy_1	NP_414546_near_copy_2	99	100	99	98	98	100.00	  197
-NP_414546_near_copy_2	NP_414546_near_copy_1	100	99	98	99	98	100.00	  197
+gi|16127997|ref|NP_414544.1|	NP_414544_near_copy	310	309	99	100	309	99.68	638
+NP_414544_near_copy	gi|16127997|ref|NP_414544.1|	309	310	100	99	309	99.68	638
+NP_414546_near_copy_1	NP_414546_near_copy_2	99	100	99	98	98	100.00	197
+NP_414546_near_copy_2	NP_414546_near_copy_1	100	99	98	99	98	100.00	197
diff -r b41f8c43705e -r 75ab3e2cfa0e test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular
--- a/test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular	Fri Sep 04 07:05:56 2015 -0400
+++ b/test-data/rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular	Mon Sep 07 04:40:02 2015 -0400
@@ -1,2 +1,2 @@
 #A_id	B_id	A_length	B_length	A_qcovhsp	B_qcovhsp	length	pident	bitscore
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	1047	1213	100	86	1047	92.07	 1474
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	1047	1213	100	86	1047	92.07	1474
diff -r b41f8c43705e -r 75ab3e2cfa0e test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular
--- a/test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular	Fri Sep 04 07:05:56 2015 -0400
+++ b/test-data/rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular	Mon Sep 07 04:40:02 2015 -0400
@@ -1,2 +1,2 @@
 #A_id	B_id	A_length	B_length	A_qcovhsp	B_qcovhsp	length	pident	bitscore
-gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	1047	1213	22	19	230	97.39	  559
+gi|57163782|ref|NM_001009242.1|	ENA|BC112106|BC112106.1	1047	1213	22	19	230	97.39	559
diff -r b41f8c43705e -r 75ab3e2cfa0e tools/blast_rbh/README.rst
--- a/tools/blast_rbh/README.rst	Fri Sep 04 07:05:56 2015 -0400
+++ b/tools/blast_rbh/README.rst	Mon Sep 07 04:40:02 2015 -0400
@@ -84,6 +84,7 @@
 v0.1.7  - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
         - Updated citation information with GigaScience paper.
+v0.1.8  - Updated to depend on  NCBI BLAST+ 2.2.31 via ToolShed install.
 ======= ======================================================================
 
 
@@ -97,12 +98,12 @@
 Planemo commands (which requires you have set your Tool Shed access details in
 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
     ...
 
 or::
 
-    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/galaxy_blast/tools/blast_rbh/
     ...
 
 To just build and check the tar ball, use::
diff -r b41f8c43705e -r 75ab3e2cfa0e tools/blast_rbh/blast_rbh.xml
--- a/tools/blast_rbh/blast_rbh.xml	Fri Sep 04 07:05:56 2015 -0400
+++ b/tools/blast_rbh/blast_rbh.xml	Mon Sep 07 04:40:02 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.7">
+<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.8">
     <description>from two FASTA files</description>
     <requirements>
         <requirement type="package" version="1.64">biopython</requirement>
@@ -6,7 +6,7 @@
         <requirement type="binary">makeblastdb</requirement>
         <requirement type="binary">blastp</requirement>
         <requirement type="binary">blastn</requirement>
-        <requirement type="package" version="2.2.30">blast+</requirement>
+        <requirement type="package" version="2.2.31">blast+</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
diff -r b41f8c43705e -r 75ab3e2cfa0e tools/blast_rbh/tool_dependencies.xml
--- a/tools/blast_rbh/tool_dependencies.xml	Fri Sep 04 07:05:56 2015 -0400
+++ b/tools/blast_rbh/tool_dependencies.xml	Mon Sep 07 04:40:02 2015 -0400
@@ -3,7 +3,7 @@
     <package name="biopython" version="1.64">
         <repository changeset_revision="268128adb501" name="package_biopython_1_64" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="blast+" version="2.2.30">
-        <repository changeset_revision="f69b90d89b62" name="package_blast_plus_2_2_30" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="blast+" version="2.2.31">
+        <repository changeset_revision="a2b8e3898680" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>