# HG changeset patch
# User iuc
# Date 1729721539 0
# Node ID 04adc9db15810894930353c6b3502b74a00d0346
# Parent  22cf48ad7b16367b3c439918b626c45ae56b01e3
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit 52b81aad3194e02a04ec09eea1aa0c1e9301e942

diff -r 22cf48ad7b16 -r 04adc9db1581 cuff_macros.xml
--- a/cuff_macros.xml	Sat Oct 05 11:16:16 2024 +0000
+++ b/cuff_macros.xml	Wed Oct 23 22:12:19 2024 +0000
@@ -79,7 +79,7 @@
 #end for
     ]]></token>
     <token name="@CUFFLINKS_GTF_INPUTS@"><![CDATA[
-## Inputs.
+## Inputs. 
 #for $i, $input_file in enumerate($inputs):
     'input_$i'
 #end for
diff -r 22cf48ad7b16 -r 04adc9db1581 cuffmerge_wrapper.xml
--- a/cuffmerge_wrapper.xml	Sat Oct 05 11:16:16 2024 +0000
+++ b/cuffmerge_wrapper.xml	Wed Oct 23 22:12:19 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="cuffmerge" name="Cuffmerge" version="@TOOL_VERSION@.4" profile="@PROFILE@">
+<tool id="cuffmerge" name="Cuffmerge" version="@TOOL_VERSION@.5" profile="@PROFILE@">
     <description>merge together several Cufflinks assemblies</description>
     <macros>
       <import>cuff_macros.xml</import>
@@ -7,7 +7,7 @@
     <version_command>cuffmerge -v</version_command>
     <command detect_errors="aggressive"><![CDATA[
         @CUFFLINKS_LINK_GTF_INPUTS@
-        echo @CUFFLINKS_GTF_INPUTS@ | sed 's/\s\+/\n/' > assembly_GTF_list.txt &&
+        echo @CUFFLINKS_GTF_INPUTS@ | sed 's/\s\+/\n/g' > assembly_GTF_list.txt &&
         cuffmerge 
             -o output
             --num-threads="\${GALAXY_SLOTS:-4}"