Mercurial > repos > galaxyp > morpheus

changeset 2:1c8071d2ae6f draft

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Uploaded
author galaxyp
date Thu, 05 Nov 2015 09:22:08 -0500
parents a5a1c3367774
children 12c5c3a50d4b
files morpheus.xml
diffstat 1 files changed, 1 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/morpheus.xml	Thu Nov 05 09:09:04 2015 -0500
+++ b/morpheus.xml	Thu Nov 05 09:22:08 2015 -0500
@@ -132,7 +132,7 @@
         -mt=\${GALAXY_SLOTS:-4}
         && ( basepath=`grep 'Input Data File:' input.log.txt | sed 's/Input Data File: \(.*\)input.mzml/\1/'`; 
              for i in summary.tsv input.log.txt input.PSMs.tsv input.unique_peptides.tsv input.protein_groups.tsv input.pep.xml; 
-             do cat \$i | sed "s#\${basepath}input.mzml#$input.name#" | sed "s#\${basepath}$searchdb_name#$search.name#" > output_reports/\$i; 
+             do cat \$i | sed "s#\${basepath}input.mzml#$input.name#" | sed "s#\${basepath}$searchdb_name#$searchdb.name#" > output_reports/\$i; 
              done )
     ]]></command>
     <inputs>