# HG changeset patch
# User bgruening
# Date 1377975605 14400
# Node ID c650ee099c51ce9e1e42439af105188ed8dd7f0d
# Parent  2b3adbe83979b5a541c7bae4ab2d7fb0e07cacee
Uploaded

diff -r 2b3adbe83979 -r c650ee099c51 cmsearch.xml
--- a/cmsearch.xml	Sat Aug 31 09:58:04 2013 -0400
+++ b/cmsearch.xml	Sat Aug 31 15:00:05 2013 -0400
@@ -5,9 +5,7 @@
         <requirement type="package" version="1.1rc4">infernal</requirement>
     </requirements>
     <command>
-        ##TODO reformat the tabular-output: 
-        ## -"Each line consists of 18 space-delimited fields followed by a free text target sequence description, as follows:"
-        ## remove line that starts with #
+        temp_tabular_output=$(mktemp);
 
         cmsearch 
             --cpu 12
@@ -21,7 +19,7 @@
             $nohmm
             $mid
             $bitscore_thresholds
-            --tblout $outfile
+            --tblout $temp_tabular_output
             $g
             #if $A:
                 $A $multiple_alignment_output
@@ -29,13 +27,13 @@
 
             #if $inclusion_thresholds_opts.inclusion_thresholds_selector == "--incE":
                 --incE $inclusion_thresholds_opts.incE
-            #else:
+            #elif $inclusion_thresholds_opts.inclusion_thresholds_selector == "--incT":
                 --incT $inclusion_thresholds_opts.incT
             #end if
 
             #if $reporting_thresholds_opts.reporting_thresholds_selector == "-E":
                 -E $reporting_thresholds_opts.E
-            #else:
+            #elif $reporting_thresholds_opts.reporting_thresholds_selector == "-T":
                 -T $reporting_thresholds_opts.T
             #end if
 
@@ -46,9 +44,11 @@
             #end if
 
             $seqdb
-
+            2>&#38;1
+            ;
 
-            2>&#38;1
+            sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' $temp_tabular_output > $outfile
+
     </command>
         <inputs>
 
@@ -117,9 +117,11 @@
             <conditional name="inclusion_thresholds_opts">
                 <param name="inclusion_thresholds_selector" type="select" label="Inclusion thresholds"
                 help="Inclusion thresholds are stricter than reporting thresholds. Inclusion thresholds control which hits are considered to be reliable enough to be included in an output alignment or in a possible subsequent search round, or marked as significant (”!”) as opposed to questionable (”?”) in hit output.">
-                    <option value="--incE" selected="true">Use E-value</option>
+                    <option value="" selected="true">default</option>
+                    <option value="--incE">Use E-value</option>
                     <option value="--incT">Use bit score</option>
                 </param>
+                <when />
                 <when value="--incE">
                     <param name="incE" type="float" value="0.01" size="5" label="Use E-value" help="of &lt;= X as the hit inclusion threshold.">
                         <sanitizer>
@@ -140,15 +142,16 @@
                 </when>
             </conditional>
 
-
             <!-- Options controlling reporting thresholds -->
 
             <conditional name="reporting_thresholds_opts">
                 <param name="reporting_thresholds_selector" type="select" label="reporting thresholds"
                 help="Reporting thresholds control which hits are reported in output files">
-                    <option value="-E" selected="true">Use E-value</option>
+                    <option value="" selected="true">default</option>
+                    <option value="-E">Use E-value</option>
                     <option value="-T">Use bit score</option>
                 </param>
+                <when />
                 <when value="-E">
                     <param name="E" type="float" value="10.0" size="5" label="Use E-value" help="of &lt;= X as the hit reporting threshold. The default is 10.0, meaning that on average, about 10 false positives will be reported per query, so you can see the top of the noise and decide for yourself if it’s really noise.">
                         <sanitizer>
@@ -172,7 +175,6 @@
             <param name="A" truevalue="-A" falsevalue="" checked="False" type="boolean" 
                 label="Save a multiple alignment of all significant hits" help="... those satisfying inclusion thresholds"/>
 
-
         </inputs>
     <outputs>