# HG changeset patch
# User devteam
# Date 1442410771 14400
# Node ID 5ce5197de50c12656a7bc592f0dc9cc65e76dc11
# Parent  4e6f043995ff09d0c69f94b9278cfff2b9897bd0
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffdiff commit 220e70acb66016873732b193b3ac20ae48083f0b-dirty

diff -r 4e6f043995ff -r 5ce5197de50c cuff_macros.xml
--- a/cuff_macros.xml	Wed Jun 03 15:04:19 2015 -0400
+++ b/cuff_macros.xml	Wed Sep 16 09:39:31 2015 -0400
@@ -10,8 +10,8 @@
     <stdio>
         <exit_code range="1:" />
         <exit_code range=":-1" />
-        <regex match="Error:" />
-        <regex match="Exception:" />
+        <regex match="Error" />
+        <regex match="Exception" />
     </stdio>
   </xml>
   <xml name="condition_inputs">
@@ -88,4 +88,4 @@
             #end for
   </token>
   <token name="@HAS_MULTIPLE_INPUTS@">getattr(inputs, "__len__", [].__len__)() >= 2</token>
-</macros>
\ No newline at end of file
+</macros>
diff -r 4e6f043995ff -r 5ce5197de50c cuffdiff_wrapper.xml
--- a/cuffdiff_wrapper.xml	Wed Jun 03 15:04:19 2015 -0400
+++ b/cuffdiff_wrapper.xml	Wed Sep 16 09:39:31 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.2">
+<tool id="cuffdiff" name="Cuffdiff" version="@VERSION@.3">
     <description>find significant changes in transcript expression, splicing, and promoter use</description>
     <requirements>
         <requirement type="set_environment">CUFFDIFF_SCRIPT_PATH</requirement>
@@ -203,10 +203,10 @@
         <data format="tabular" name="tss_groups_read_group" label="${tool.name} on ${on_string}: TSS groups read group tracking" from_work_dir="tss_groups.read_group_tracking" >
             <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
         </data>
-        <data format="text" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" >
+        <data format="txt" name="read_group_info" label="${tool.name} on ${on_string}: read group info" from_work_dir="read_groups.info" >
             <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
         </data>
-        <data format="text" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" >
+        <data format="txt" name="run_info" label="${tool.name} on ${on_string}: run info" from_work_dir="run.info" >
             <filter>(include_read_group_files == 'Yes') and not omit_tabular_output</filter>
         </data>
         <!-- Standard datasets. -->
diff -r 4e6f043995ff -r 5ce5197de50c tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Jun 03 15:04:19 2015 -0400
+++ b/tool_dependencies.xml	Wed Sep 16 09:39:31 2015 -0400
@@ -7,6 +7,6 @@
         <repository changeset_revision="899067a260d1" name="package_cufflinks_2_2_1" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="cummeRbund" version="2.8.2">
-        <repository changeset_revision="f18bcdb8c6c5" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="13c270433440" name="package_cummerbund_2_8_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>