# HG changeset patch
# User bgruening
# Date 1377953068 14400
# Node ID a5ef9159caa955323920ecff64d61d14b65a080b
# Parent  468be760eba372789408bb84dbc168e243e3900e
Uploaded

diff -r 468be760eba3 -r a5ef9159caa9 cmsearch.xml
--- a/cmsearch.xml	Sat Aug 31 08:11:53 2013 -0400
+++ b/cmsearch.xml	Sat Aug 31 08:44:28 2013 -0400
@@ -30,9 +30,9 @@
             #end if
 
             #if $reporting_thresholds_opts.reporting_thresholds_selector == "-E":
-                -E $inclusion_thresholds_opts.E
+                -E $reporting_thresholds_opts.E
             #else:
-                -T $inclusion_thresholds_opts.T
+                -T $reporting_thresholds_opts.T
             #end if
 
             #if $cm_opts.cm_opts_selector == "db":
@@ -48,7 +48,7 @@
     </command>
         <inputs>
 
-            <param name="seqdb" type="data" format="fasta,embl,genbank" label="Sequence database"/>
+            <param name="seqdb" type="data" format="fasta" label="Sequence database"/>
 
             <conditional name="cm_opts">
                 <param name="cm_opts_selector" type="select" label="Subject covariance models">
@@ -65,12 +65,12 @@
                     </param>
                 </when>
                 <when value="histdb">
-                    <param name="cmfile" type="data" format="fasta" label="Covariance models"/>
+                    <param name="cmfile" type="data" format="fasta" label="Covariance models file from the history."/>
                 </when>
             </conditional>
 
             <param name="g" truevalue="-g" falsevalue="" checked="False" type="boolean" 
-                label="Turn on the glocal alignment algorithm ..." help="... global with respect to the query model and local with respect to the target database."/>
+                label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
 
             <param name="bottomonly" truevalue="--bottomonly" falsevalue="" checked="False" type="boolean" 
                 label="Only search the bottom (Crick) strand of target sequences" help="in the sequence database"/>
diff -r 468be760eba3 -r a5ef9159caa9 tool-data/infernal.loc.sample
--- a/tool-data/infernal.loc.sample	Sat Aug 31 08:11:53 2013 -0400
+++ b/tool-data/infernal.loc.sample	Sat Aug 31 08:44:28 2013 -0400
@@ -9,7 +9,7 @@
 #Your homer.loc file should include an entry per line for each "base name" 
 #you have stored.  For example:
 #
-#rfam01	RFAM 4.2 08 Aug 2013		/data/0/galaxy_data/infernal/08_08_2013/rfam.cm
+#rfam01	RFAM 4.2 08 Aug 2013	/data/0/galaxy_data/infernal/08_08_2013/rfam.cm
 #
 #...etc...
 #