format hmmer output to tabular

bgruening · Mar 7, 2024 · 3ee1072 · 3ee1072
1 parent f69e2a4
commit 3ee1072
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diff --git a/tools/rna_tools/cmsearch_deoverlap/cmsearch-deoverlap.xml b/tools/rna_tools/cmsearch_deoverlap/cmsearch-deoverlap.xml
@@ -1,4 +1,4 @@
-<tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy0" profile="21.05">
+<tool id="cmsearch_deoverlap" name="CMsearch deoverlap" version="0.08+galaxy1" profile="21.05">
     <description>removes lower scoring overlaps from cmsearch results</description>
     <requirements>
         <requirement type="package" version="5.26">perl</requirement>
@@ -13,9 +13,11 @@
         #end if
         #if $dirty:
             $dirty &&
+            sed -i 's/ \{1,\}/\t/g' *.sort &&
             mv *.sort '$matches_sort'
         #end if
         &&
+        sed -i 's/ \{1,\}/\t/g' *.deoverlapped &&
         mv *.deoverlapped '$deoverlapped_matches'
 
     ]]></command>