--- a/locarna_pairwise.xml	Wed Dec 28 18:53:24 2016 -0500
+++ b/locarna_pairwise.xml	Fri Jan 13 16:49:33 2017 -0500
@@ -1,6 +1,6 @@
-<tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.0">
+<tool id="locarna_pairwise" name="LocARNA Pairwise Aligner" version="@VERSION@.1">
     <description>
-        Pairwise Simultaneous Alignment and Folding of RNAs
+        Pairwise Simultaneous Alignment and Folding of RNAs (locarna, sparse)
     </description>
 
     <macros>
@@ -40,52 +40,16 @@
         --struct-local on
     #end if
 
-    ## -------------------- scoring parameters
-    
-    --indel $Scoring.indel
-    --indel-opening $Scoring.indel_opening
-    --struct-weight $Scoring.struct_weight
-    --tau $Scoring.tau
-    
-    #if str($Scoring.sequence_score.sequence_score_selector) == "match"
-        --match $Scoring.sequence_score.match
-        --mismatch $Scoring.sequence_score.mismatch
-    #else if str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
-        --use-ribosum true
-    #else if str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
-        --ribofit true
-    #end if
+    @SCORING_ARGS@
 
-    ## -------------------- folding parameters
-
-    #if float($Folding.rnafold_temperature) != 37.0
-        --rnafold-temperature $Folding.rnafold_temperature
-    #end if
-
+    @FOLDING_ARGS@
     $Folding.alifold_consensus_dp
     --consensus-structure $Folding.consensus_structure
 
-    ## -------------------- heuristic parameters
-    
-    -p $Heuristics.min_prob
-    --max-diff-am $Heuristics.max_diff_am
-    --max-diff $Heuristics.max_diff
-    --max-diff-at-am $Heuristics.max_diff_at_am
-    
-    #if float($Heuristics.max_bps_length_ratio) != 0.0
-        --max-bps-length-ratio $Heuristics.max_bps_length_ratio
-    #end if
+    @HEURISTIC_ARGS@
     
-    ## -------------------- other parameters
-        
-    $Constraint.lonely_pairs
-
-    #if $Constraint.maxBPspan != -1
-        --maxBPspan $Constraint.maxBPspan
-    #end if
-
-    $Constraint.ignore_constraints
-
+    @CONSTRAINT_ARGS@
+    
     ## -------------------- output
     
     #if 'stockholm' in str($outputs).split(",")
@@ -101,18 +65,15 @@
         --pp '$pp'
     #end if
     
-    $stdout_verbosity
-
-    #if str($stdout_verbosity) != "--quiet":
-        > '$stdout'
-    #end if
+    @STDOUT_ARGS@
 
     #if 'clustal' in str($outputs).split(",") and 'clustal_strict' in str($outputs).split(",")
         && cp $clustal $clustal_strict
     #end if
 
     #if 'clustal_strict' in str($outputs).split(",")
-        && sed -i '/\^#/d' '$clustal_strict'
+        && cp '$clustal_strict' '$clustal_strict~'
+        && sed '/^#/d' '$clustal_strict~' >'$clustal_strict'
     #end if
 
     ]]></command>
@@ -200,17 +161,16 @@
 
         <section name="Heuristics" title="Heuristic parameters">
             <expand macro="common_heuristic_parameters" />
+            <expand macro="max_diff_parameters_aln" />
         </section>
 
-        <section name="Constraint" title="Constraint parameters">
-            <expand macro="constraints" />
+        <section name="Constraints" title="Constraint parameters">
+            <expand macro="common_constraint_parameters" />
         </section>
     </inputs>
     
     <outputs>
-        <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
-            <filter>stdout_verbosity != '--quiet'</filter>
-        </data>
+        <expand macro="standard_outupt" />
         <data format="clustal" name="clustal"
               label="${tool.name} alignment (annotated clustal) on ${on_string}">
             <filter>'clustal' in outputs</filter>
@@ -234,7 +194,14 @@
             <param name="inputA" value="tRNA_2-1.fa" />
             <param name="inputB" value="tRNA_2-2.fa" />
             <param name="outputs" value="clustal" />
-            <output name="clustal" file="tRNA_2.aln" />
+            <output name="clustal" file="tRNA_2.aln" lines_diff="2" />
+        </test>
+        <test>
+            <param name="inputA" value="haca.snoRNA-1.aln" />
+            <param name="inputB" value="haca.snoRNA-2.aln" />
+            <param name="outputs" value="clustal_strict,clustal" />
+            <output name="clustal" file="haca.snoRNA-c.aln" lines_diff="2" />
+            <output name="clustal_strict" file="haca.snoRNA.aln" lines_diff="1" />
         </test>
     </tests>