# HG changeset patch
# User bgruening
# Date 1364750224 14400
# Node ID 512145f2e41738d42490aebcae2fba626b24440a
# Parent  b216c5c94dd18e1bc8fa1235d2654bb08332d561
Uploaded

diff -r b216c5c94dd1 -r 512145f2e417 simsearch.xml
--- a/simsearch.xml	Wed Mar 27 15:28:31 2013 -0400
+++ b/simsearch.xml	Sun Mar 31 13:17:04 2013 -0400
@@ -7,7 +7,7 @@
     <command>
         #if $method_opts.method_opts_selector == "chemfp":
             ## TODO: remove all comment lines, in muti mode many comment lines will be appear, also in the middle of the result file, remove them
-            simsearch -k $method_opts.k --threshold $method_opts.threshold --in fps --target-format fps -q "${method_opts.query}" "${method_opts.targets}" -o "${outfile}"
+            simsearch -k $method_opts.k --threshold $method_opts.threshold --query-format fps --target-format fps -q "${method_opts.query}" "${method_opts.targets}" -o "${outfile}"
         #else:
             ## OpenBabel needs the original molecule file (molecule.'fileformat') next to the fastsearch index (molecule.fs). We use a composite datatype to accomplish that.
             ## Furthermore OpenBabel is really picky with fileextensions. We need to specify every datatype. I did not find a solution to specify the query-filetype.
diff -r b216c5c94dd1 -r 512145f2e417 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 27 15:28:31 2013 -0400
+++ b/tool_dependencies.xml	Sun Mar 31 13:17:04 2013 -0400
@@ -1,8 +1,8 @@
 <tool_dependency>
     <package name="openbabel" version="2.3.2">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="9e07452137da" />
+	<repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="package_openbabel_2_3" owner="bgruening" changeset_revision="9e07452137da" />
     </package>
     <package name="chemfp" version="1.1p1">
-        <repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="chemfp" owner="bgruening" changeset_revision="da72072c9710" />
+	<repository toolshed="http://testtoolshed.g2.bx.psu.edu/" name="chemfp" owner="bgruening" changeset_revision="a4e261ee0a51" />
     </package>
 </tool_dependency>