# HG changeset patch
# User peterjc
# Date 1494437086 14400
# Node ID a06ad07431baac48d0ac0bd5a97dbd0b3bb55aea
# Parent  09a8be9247caedd6a50386bb7f304ce679a0e2ac
v0.2.1 Adds table 24; Depends on Biopython 1.67 via Tool Shed package or bioconda.

diff -r 09a8be9247ca -r a06ad07431ba tools/get_orfs_or_cdss/README.rst
--- a/tools/get_orfs_or_cdss/README.rst	Sat Jan 09 23:42:32 2016 -0500
+++ b/tools/get_orfs_or_cdss/README.rst	Wed May 10 13:24:46 2017 -0400
@@ -1,7 +1,7 @@
 Galaxy tool to find ORFs or simple CDSs
 =======================================
 
-This tool is copyright 2011-2015 by Peter Cock, The James Hutton Institute
+This tool is copyright 2011-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 Additions copyright 2015-2016 by Eric Rasche.
 See the licence text below (MIT licence).
@@ -77,6 +77,9 @@
         - Added NCBI genetic code table 24, Pterobranchia Mitochondrial.
 v0.1.1  - Reorder XML elements (internal change only).
 v0.2.0  - Tool now also outputs GFF3 formatted calls (Eric Rasche).
+v0.2.1  - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
+        - Added NCBI genetic code table 24, Candidate Division SR1 and
+	  Gracilibacteria.
 ======= ======================================================================
 
 
@@ -93,17 +96,17 @@
 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 -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
+    $ planemo shed_update -t testtoolshed --check_diff tools/get_orfs_or_cdss/
     ...
 
 or::
 
-    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
+    $ planemo shed_update -t toolshed --check_diff tools/get_orfs_or_cdss/
     ...
 
 To just build and check the tar ball, use::
 
-    $ planemo shed_upload --tar_only  ~/repositories/pico_galaxy/tools/get_orfs_or_cdss/
+    $ planemo shed_upload --tar_only tools/get_orfs_or_cdss/
     ...
     $ tar -tzf shed_upload.tar.gz
     test-data/Ssuis.fasta
diff -r 09a8be9247ca -r a06ad07431ba tools/get_orfs_or_cdss/get_orfs_or_cdss.py
--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.py	Sat Jan 09 23:42:32 2016 -0500
+++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.py	Wed May 10 13:24:46 2017 -0400
@@ -17,8 +17,10 @@
 
 See accompanying text file for licence details (MIT licence).
 """
+
+import re
 import sys
-import re
+
 from optparse import OptionParser
 
 usage = """Use as follows:
@@ -210,6 +212,7 @@
         raise StopIteration
     yield values[0]
 
+
 if options.mode == "all":
     get_peptides = get_all_peptides
 elif options.mode == "top":
diff -r 09a8be9247ca -r a06ad07431ba tools/get_orfs_or_cdss/get_orfs_or_cdss.xml
--- a/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml	Sat Jan 09 23:42:32 2016 -0500
+++ b/tools/get_orfs_or_cdss/get_orfs_or_cdss.xml	Wed May 10 13:24:46 2017 -0400
@@ -1,8 +1,7 @@
-<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.0">
+<tool id="get_orfs_or_cdss" name="Get open reading frames (ORFs) or coding sequences (CDSs)" version="0.2.1">
     <description>e.g. to get peptides from ESTs</description>
     <requirements>
-        <requirement type="package" version="1.65">biopython</requirement>
-        <requirement type="python-module">Bio</requirement>
+        <requirement type="package" version="1.67">biopython</requirement>
     </requirements>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -34,6 +33,15 @@
             <option value="22">22. Scenedesmus obliquus</option>
             <option value="23">23. Thraustochytrium Mitochondrial</option>
             <option value="24">24. Pterobranchia Mitochondrial</option>
+            <option value="25">25. Candidate Division SR1 and Gracilibacteria</option>
+            <!-- TODO, these are not in Biopython 1.67
+            <option value="26">26. Pachysolen tannophilus Nuclear</option>
+            <option value="26">27. Karyorelict Nuclear</option>
+            <option value="26">28. Condylostoma Nuclear</option>
+            <option value="26">29. Mesodinium Nuclear</option>
+            <option value="26">30. Peritrich Nuclear</option>
+            <option value="26">31. Blastocrithidia Nuclear</option>
+            -->
         </param>
         <param name="ftype" type="select" value="True" label="Look for ORFs or CDSs">
             <option value="ORF">Look for ORFs (check for stop codons only, ignore start codons)</option>
diff -r 09a8be9247ca -r a06ad07431ba tools/get_orfs_or_cdss/tool_dependencies.xml
--- a/tools/get_orfs_or_cdss/tool_dependencies.xml	Sat Jan 09 23:42:32 2016 -0500
+++ b/tools/get_orfs_or_cdss/tool_dependencies.xml	Wed May 10 13:24:46 2017 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="biopython" version="1.65">
-        <repository changeset_revision="030f1a505d40" name="package_biopython_1_65" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="biopython" version="1.67">
+        <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>