# HG changeset patch
# User peterjc
# Date 1441110289 14400
# Node ID 22e71e53f534e463380da1c3743be4d229b624ee
# Parent  9e36a1b9302d4cdb02e9cbc228625ae797140466
Capture version of promoter2

diff -r 9e36a1b9302d -r 22e71e53f534 tools/protein_analysis/README.rst
--- a/tools/protein_analysis/README.rst	Thu May 21 10:57:40 2015 -0400
+++ b/tools/protein_analysis/README.rst	Tue Sep 01 08:24:49 2015 -0400
@@ -177,6 +177,7 @@
 v0.2.7  - Style cleanup in Python scripts.
 v0.2.8  - Reorder XML elements (internal change only).
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+        - Record version of Promoter 2 via ``<version_command>``.
 ======= ======================================================================
 
 
@@ -195,12 +196,12 @@
 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/pico_galaxy/tools/protein_analysis/
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
     ...
 
 or::
 
-    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/protein_analysis/
     ...
 
 To just build and check the tar ball, use::
diff -r 9e36a1b9302d -r 22e71e53f534 tools/protein_analysis/promoter2.py
--- a/tools/protein_analysis/promoter2.py	Thu May 21 10:57:40 2015 -0400
+++ b/tools/protein_analysis/promoter2.py	Tue Sep 01 08:24:49 2015 -0400
@@ -34,6 +34,9 @@
 
 FASTA_CHUNK = 500
 
+if "-v" in sys.argv or "--version" in sys.argv:
+    sys.exit(os.system("promoter -V"))
+
 if len(sys.argv) != 4:
     sys_exit("Require three arguments, number of threads (int), input DNA FASTA file & output tabular file. "
              "Got %i arguments." % (len(sys.argv)-1))
diff -r 9e36a1b9302d -r 22e71e53f534 tools/protein_analysis/promoter2.xml
--- a/tools/protein_analysis/promoter2.xml	Thu May 21 10:57:40 2015 -0400
+++ b/tools/protein_analysis/promoter2.xml	Tue Sep 01 08:24:49 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="promoter2" name="Promoter 2.0" version="0.0.9">
+<tool id="promoter2" name="Promoter 2.0" version="0.0.10">
     <description>Find eukaryotic PolII promoters in DNA sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
@@ -12,6 +12,7 @@
         <exit_code range="1:" />
         <exit_code range=":-1" />
     </stdio>
+    <version_command interpreter="python">promoter2.py --version</version_command>
     <command interpreter="python">
         promoter2.py "\$GALAXY_SLOTS" "$fasta_file" "$tabular_file"
         ##If the environment variable isn't set, get "", and the python wrapper