# HG changeset patch
# User bgruening
# Date 1378637298 14400
# Node ID 5c6344f67ad08931c4ae68cd99323539ad10aeab
# Parent  0bffd41833267d010cfaf2420f1907f81d1960e9
Uploaded

diff -r 0bffd4183326 -r 5c6344f67ad0 cmbuild.xml
--- a/cmbuild.xml	Sun Sep 08 05:08:20 2013 -0400
+++ b/cmbuild.xml	Sun Sep 08 06:48:18 2013 -0400
@@ -28,14 +28,14 @@
             #end if
 
             $effective_opts.effective_opts_selector
-            #if $effective_opts.effective_opts_selector == '--eent':
+            #if str($effective_opts.effective_opts_selector) == '--eent':
                 --ere $effective_opts.ere
                 --eminseq $effective_opts.eminseq
                 --ehmmre $effective_opts.ehmmre
                 --eset $effective_opts.eset
             #end if
 
-            #if $refining_opts.refining_opts_selector == '--refine':
+            #if str($refining_opts.refining_opts_selector) == '--refine':
                 #if $refining_opts.refine_output:
                     --refine $refined_multiple_alignment_output
                 #else:
@@ -45,7 +45,7 @@
                 $l
                 $refining_opts.gibbs_opts.gibbs_opts_selector
 
-                #if $refining_opts.gibbs_opts.gibbs_opts_selector == '--gibbs':
+                #if str($refining_opts.gibbs_opts.gibbs_opts_selector) == '--gibbs':
                     $refining_opts.gibbs_opts.random_seed
                 #end if
 
diff -r 0bffd4183326 -r 5c6344f67ad0 cmsearch.xml
--- a/cmsearch.xml	Sun Sep 08 05:08:20 2013 -0400
+++ b/cmsearch.xml	Sun Sep 08 06:48:18 2013 -0400
@@ -30,21 +30,21 @@
                 $A $multiple_alignment_output
             #end if
 
-            #if $inclusion_thresholds_opts.inclusion_thresholds_selector == "--incE":
+            #if str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incE":
                 --incE $inclusion_thresholds_opts.incE
-            #elif $inclusion_thresholds_opts.inclusion_thresholds_selector == "--incT":
+            #elif str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incT":
                 --incT $inclusion_thresholds_opts.incT
             #end if
 
-            #if $reporting_thresholds_opts.reporting_thresholds_selector == "-E":
+            #if str($reporting_thresholds_opts.reporting_thresholds_selector) == "-E":
                 -E $reporting_thresholds_opts.E
-            #elif $reporting_thresholds_opts.reporting_thresholds_selector == "-T":
+            #elif str($reporting_thresholds_opts.reporting_thresholds_selector) == "-T":
                 -T $reporting_thresholds_opts.T
             #end if
 
             ## CM file from the history or stored as database on disc
 
-            #if $cm_opts.cm_opts_selector == "db":
+            #if str($cm_opts.cm_opts_selector) == "db":
                 $cm_opts.database.fields.path
             #else:
                 $cm_opts.cmfile
diff -r 0bffd4183326 -r 5c6344f67ad0 cmstat.xml
--- a/cmstat.xml	Sun Sep 08 05:08:20 2013 -0400
+++ b/cmstat.xml	Sun Sep 08 06:48:18 2013 -0400
@@ -12,7 +12,7 @@
 
         cmstat
 
-            #if $cm_opts.cm_opts_selector == "db":
+            #if str($cm_opts.cm_opts_selector) == "db":
                 $cm_opts.database.fields.path
             #else:
                 $cm_opts.cmfile
@@ -47,7 +47,7 @@
             </conditional>
         </inputs>
     <outputs>
-        <data format="tabular" name="outfile" label="cmsearch on ${on_string}"/>
+        <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
     </outputs>
     <help>