# HG changeset patch
# User rnateam
# Date 1710779559 0
# Node ID 874ad23526a09242a13c68ea9f93a5c272ca6eac
# Parent  3fd3be28a04c495312d261f7888e4c5bd7b05241
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/cmsearch_deoverlap commit fa7deee70d449c6ec1ae9eb42d01d283e9bee586

diff -r 3fd3be28a04c -r 874ad23526a0 cmsearch-deoverlap.xml
--- a/cmsearch-deoverlap.xml	Mon Mar 18 09:34:56 2024 +0000
+++ b/cmsearch-deoverlap.xml	Mon Mar 18 16:32:39 2024 +0000
@@ -1,7 +1,11 @@
-<tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy1" profile="21.05">
+<tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy2" profile="21.05">
     <description>removes lower scoring overlaps from cmsearch results</description>
+    <xrefs>
+	<xref type="bio.tools">cmsearch-deoverlap</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="5.26">perl</requirement>
+	<requirement type="package" version="4.8">sed</requirement>
     </requirements>
     <command><![CDATA[
         ln -s '$clan_information' clan_info &&
@@ -13,11 +17,11 @@
         #end if
         #if $dirty:
             $dirty &&
-            sed 's/[:blank:]+/,/g' cmsearch_matches.sort > cmsearch_matches.sort.tabular &&
+            sed "s/[[:blank:]]\+/\t/g" cmsearch_matches.sort > cmsearch_matches.sort.tabular &&
             mv cmsearch_matches.sort.tabular '$matches_sort'
         #end if
         &&
-        sed 's/[:blank:]+/,/g' cmsearch_matches.deoverlapped > cmsearch_matches.deoverlapped.tabular &&
+        sed "s/[[:blank:]]\+/\t/g" cmsearch_matches.deoverlapped > cmsearch_matches.deoverlapped.tabular &&
         mv cmsearch_matches.deoverlapped.tabular '$deoverlapped_matches'
 
     ]]></command>