# HG changeset patch
# User devteam
# Date 1487524358 18000
# Node ID cf747d1bd79aa3a827ab36ce448f98271fef09fb
# Parent  1707a530e598e335728f903750cb2e5fcd1953a7
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffmerge commit 82ee6fc860c52c531b7a57bbb346ab1a67a434a5

diff -r 1707a530e598 -r cf747d1bd79a cuff_macros.xml
--- a/cuff_macros.xml	Tue Feb 07 18:39:42 2017 -0500
+++ b/cuff_macros.xml	Sun Feb 19 12:12:38 2017 -0500
@@ -8,14 +8,6 @@
     </requirements>
   </xml>
 
-  <xml name="stdio">
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <regex match="Error" />
-        <regex match="Exception" />
-    </stdio>
-  </xml>
   <xml name="condition_inputs">
     <!-- DEFAULT : use BAM/SAM files -->
     <conditional name="in_type">
diff -r 1707a530e598 -r cf747d1bd79a cuffmerge_wrapper.py
--- a/cuffmerge_wrapper.py	Tue Feb 07 18:39:42 2017 -0500
+++ b/cuffmerge_wrapper.py	Sun Feb 19 12:12:38 2017 -0500
@@ -29,23 +29,6 @@
 
     (options, args) = parser.parse_args()
 
-    # output version # of tool
-    try:
-        with tempfile.NamedTemporaryFile() as tmp_stdout:
-            returncode = subprocess.call(args='cuffmerge -v 2>&1', stdout=tmp_stdout, shell=True)
-            stdout = None
-            with open(tmp_stdout.name) as tmp_stdout2:
-                for line in tmp_stdout2:
-                    if line.lower().find('merge_cuff_asms v') >= 0:
-                        stdout = line.strip()
-                        break
-        if stdout:
-            sys.stdout.write('%s\n' % stdout)
-        else:
-            raise Exception
-    except:
-        sys.stdout.write('Could not determine Cuffmerge version\n')
-
     # Set/link to sequence file.
     if options.use_seq_data:
         if options.ref_file:
diff -r 1707a530e598 -r cf747d1bd79a cuffmerge_wrapper.xml
--- a/cuffmerge_wrapper.xml	Tue Feb 07 18:39:42 2017 -0500
+++ b/cuffmerge_wrapper.xml	Sun Feb 19 12:12:38 2017 -0500
@@ -1,11 +1,11 @@
-<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.0">
+<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.1">
     <description>merge together several Cufflinks assemblies</description>
     <macros>
       <import>cuff_macros.xml</import>
     </macros>
     <expand macro="requirements" />
-    <expand macro="stdio" />
-    <command>
+     <version_command>cuffmerge -v</version_command>
+    <command detect_errors="aggressive">
         python '$__tool_directory__/cuffmerge_wrapper.py'
             --num-threads="\${GALAXY_SLOTS:-4}"
             
diff -r 1707a530e598 -r cf747d1bd79a tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 07 18:39:42 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="cufflinks" version="2.2.1">
-        <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>