# HG changeset patch
# User peterjc
# Date 1406716658 14400
# Node ID fa920e4c34631b3dc17f19c116e989ec5a14ef5e
# Parent  97151ae9eb2b779ff3bc35058776b4bff6f39c25
Uploaded v0.2.0 preview 1, fixed Biopython dependency declaration

diff -r 97151ae9eb2b -r fa920e4c3463 tools/seq_filter_by_id/README.rst
--- a/tools/seq_filter_by_id/README.rst	Wed Jun 11 11:25:26 2014 -0400
+++ b/tools/seq_filter_by_id/README.rst	Wed Jul 30 06:37:38 2014 -0400
@@ -76,6 +76,7 @@
 v0.2.0  - Can supply ID list as a text parameter (instead of in a file)
         - Using optparse for command line API.
         - Advanced option to ignore paired read suffices.
+        - Updated dependencies to use Biopython 1.64.
 ======= ======================================================================
 
 
diff -r 97151ae9eb2b -r fa920e4c3463 tools/seq_filter_by_id/seq_filter_by_id.py
--- a/tools/seq_filter_by_id/seq_filter_by_id.py	Wed Jun 11 11:25:26 2014 -0400
+++ b/tools/seq_filter_by_id/seq_filter_by_id.py	Wed Jul 30 06:37:38 2014 -0400
@@ -29,7 +29,7 @@
 (formerly the Scottish Crop Research Institute, SCRI), UK. All rights reserved.
 See accompanying text file for licence details (MIT license).
 
-This is version 0.2.0 of the script, use -v or --version to get the version.
+Use -v or --version to get the version, -h or --help for help.
 """
 import os
 import sys
@@ -40,10 +40,6 @@
     sys.stderr.write(msg.rstrip() + "\n")
     sys.exit(err)
 
-if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.2.0"
-    sys.exit(0)
-
 #Parse Command Line
 usage = """Use as follows:
 
@@ -79,7 +75,16 @@
 parser.add_option("-s", "--suffix", dest="suffix",
                   action="store_true",
                   help="Ignore pair-read suffices for matching names")
-(options, args) = parser.parse_args()
+parser.add_option("-v", "--version", dest="version",
+                  default=False, action="store_true",
+                  help="Show version and quit")
+
+options, args = parser.parse_args()
+
+if options.version:
+    print "v0.2.0"
+    sys.exit(0)
+
 in_file = options.input
 seq_format = options.format
 out_positive_file = options.output_positive
diff -r 97151ae9eb2b -r fa920e4c3463 tools/seq_filter_by_id/seq_filter_by_id.tar.gz
Binary file tools/seq_filter_by_id/seq_filter_by_id.tar.gz has changed
diff -r 97151ae9eb2b -r fa920e4c3463 tools/seq_filter_by_id/seq_filter_by_id.xml
--- a/tools/seq_filter_by_id/seq_filter_by_id.xml	Wed Jun 11 11:25:26 2014 -0400
+++ b/tools/seq_filter_by_id/seq_filter_by_id.xml	Wed Jul 30 06:37:38 2014 -0400
@@ -1,7 +1,7 @@
 <tool id="seq_filter_by_id" name="Filter sequences by ID" version="0.2.0">
     <description>from a tabular file</description>
     <requirements>
-        <requirement type="package" version="1.63">biopython</requirement>
+        <requirement type="package" version="1.64">biopython</requirement>
         <requirement type="python-module">Bio</requirement>
     </requirements>
     <version_command interpreter="python">seq_filter_by_id.py --version</version_command>
@@ -154,7 +154,7 @@
 or just the non-matching ones.
 
 Instead of providing the identifiers in a tabular file, you can alternatively
-provide them as a paramter (type or paste them into the text box). This is a
+provide them as a parameter (type or paste them into the text box). This is a
 useful shortcut for extracting a few sequences of interest without first having
 to prepare a tabular file.
 
diff -r 97151ae9eb2b -r fa920e4c3463 tools/seq_filter_by_id/tool_dependencies.xml
--- a/tools/seq_filter_by_id/tool_dependencies.xml	Wed Jun 11 11:25:26 2014 -0400
+++ b/tools/seq_filter_by_id/tool_dependencies.xml	Wed Jul 30 06:37:38 2014 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="biopython" version="1.62">
-        <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <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>
 </tool_dependency>