--- a/locarna_exparnap.xml	Sat Jan 21 17:38:46 2017 -0500
+++ b/locarna_exparnap.xml	Mon Dec 05 13:58:16 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@VERSION@.0">
+<tool id="locarna_exparnap" name="LocARNA Exact Matcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>
         Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)
     </description>
@@ -28,11 +28,13 @@
     --struct-mismatch-score $Scoring.struct_mismatch_score
 
     @HEURISTIC_ARGS@
+    --max-uil-length-ratio $Heuristics.max_uil_length_ratio
+    --max-bpil-length-ratio $Heuristics.max_bpil_length_ratio
     --prob_unpaired_in_loop_threshold $Heuristics.prob_unpaired_in_loop_threshold
     --prob_basepair_in_loop_threshold $Heuristics.prob_basepair_in_loop_threshold
 
     @CONSTRAINT_ARGS@
-
+    @FOLDING_ARGS@
     ## -------------------- other parameters
     #
     #if str($Other.subopt.subopt_selector) == "on"
@@ -94,47 +96,47 @@
                help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
                />
 
-        <param name="outputs" type="select" display="checkboxes" multiple="True"
+        <param name="outputs" type="select" display="checkboxes" multiple="true"
                label="Output options">
-            <option value="postscript" selected="False">Best EPM chain
+            <option value="postscript" selected="false">Best EPM chain
             as colored postscript</option>
-            <option value="anchors-fasta" selected="False">Fasta with anchor
+            <option value="anchors-fasta" selected="false">Fasta with anchor
             constraints from chaining</option>
-            <option value="anchors-pp" selected="False">LocARNA PP
+            <option value="anchors-pp" selected="false">LocARNA PP
             files merging input PPs and anchor constraints from
             chaining</option>
-            <option value="clustal" selected="False">Chain as
+            <option value="clustal" selected="false">Chain as
             alignment in Clustal format</option>
-            <option value="epm_list" selected="False">List of the found EPMs</option>
-            <option value="chained_epm_list" selected="False">List of
+            <option value="epm_list" selected="false">List of the found EPMs</option>
+            <option value="chained_epm_list" selected="false">List of
             EPMs in the best chain</option>
         </param>
 
         <param name="stdout_verbosity" type="select" label="Standard output verbosity">
             <option value="--quiet">Don't report standard
             output</option>
-            <option value="" selected="True">Non verbose</option>
+            <option value="" selected="true">Non verbose</option>
             <option value="--verbose">Verbose</option>
         </param>
 
         <section name="Scoring" title="Scoring parameters">
-            <param argument="alpha_1"
+            <param argument="--alpha_1"
                    type="integer" value="1" min="0" max="50"
                    label="Sequence score factor"
                    />
-            <param argument="alpha_2"
+            <param argument="--alpha_2"
                    type="integer" value="5" min="0" max="50"
                    label="Structure score factor"
                    />
-            <param name="no_stacking" argument="no-stacking" type="boolean"
+            <param argument="--no-stacking" type="boolean"
                    truevalue="" falsevalue="--no-stacking"
                    label="Add stacking terms"
                    />
-            <param argument="alpha_3"
+            <param argument="--alpha_3"
                    type="integer" value="5" min="0" max="50"
                    label="Stacking score factor"
                    />
-            <param name="struct_mismatch_score" argument="struct-mismatch-score"
+            <param argument="--struct-mismatch-score"
                    type="integer" value="-10" min="-100" max="0"
                    label="Score for nucleotide mismatch in base pair match"
                    />
@@ -167,33 +169,33 @@
                 </param>
                 <when value="off" />
                 <when value="on">
-                    <param name="diff_to_opt_score" argument="diff-to-opt-score"
+                    <param argument="--diff-to-opt-score"
                            type="integer" value="-1" min="-20" max="0"
                            label="Maximum score difference to optimum" />
-                    <param name="number_of_EPMs" argument="number-of-EPMs"
+                    <param argument="--number-of-EPMs"
                            type="integer" value="100" min="1" max="10000"
                            label="Maximal number of EPMs" />
                 </when>
             </conditional>
 
-            <param name="min_score" argument="min-score"
+            <param argument="--min-score"
                    type="integer" value="30" min="0" max="1000"
                    label="Minimum score of EPM" />
 
-            <param name="inexact_struct_match" argument="inexact-struct-match" type="boolean"
+            <param argument="--inexact-struct-match" type="boolean"
                    truevalue="--inexact-struct-match" falsevalue=""
                    label="Allow inexact structure matches"/>
 
-            <param name="add_filter" argument="add-filter" type="boolean"
-                   truevalue="--add-filter" falsevalue="" checked="False"
+            <param argument="--add-filter" type="boolean"
+                   truevalue="--add-filter" falsevalue="" checked="false"
                    label="Apply an additional filter to enumerate only
                           EPMs that are maximally extended (only inexact)"/>
 
-            <param name="no_chaining" argument="no-chaining" type="boolean"
-                   truevalue="" falsevalue="--no-chaining" checked="True"
+            <param argument="--no-chaining" type="boolean"
+                   truevalue="" falsevalue="--no-chaining" checked="true"
                    label="Find best overall chain by chaining"/>
 
-            <param name="out_min_prob" argument="out-min-prob"
+            <param argument="--out-min-prob"
                    type="float" value="0.0005" min="0" max="1"
                    label="Minimal probability in output (min-prob overrides if smaller)"/>
 
@@ -203,45 +205,51 @@
     <outputs>
         <expand macro="standard_outupt" />
         <data format="ps" name="ps_fileA"
-              label="${tool.name} chain in RNA 1 (postscript) on ${on_string}">
+              label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
             <filter>'postscript' in outputs</filter>
         </data>
         <data format="ps" name="ps_fileB"
-              label="${tool.name} chain in RNA 2 (postscript) on ${on_string}">
+              label="${tool.name} on ${on_string}: chain in RNA 2 (postscript)">
             <filter>'postscript' in outputs</filter>
         </data>
         <data format="txt" name="anchors_fasta"
-              label="${tool.name} anchor constraints from chain (fasta) on ${on_string}">
+              label="${tool.name} on ${on_string}: anchor constraints from chain (fasta)">
             <filter>'anchors-fasta' in outputs</filter>
         </data>
         <data format="txt" name="anchors_ppA"
-              label="${tool.name} anchors for RNA 1 (pp) on ${on_string}">
+              label="${tool.name} on ${on_string}: anchors for RNA 1 (pp)">
             <filter>'anchors-pp' in outputs</filter>
         </data>
         <data format="txt" name="anchors_ppB"
-              label="${tool.name} anchors for RNA 2 (pp) on ${on_string}">
+              label="${tool.name} on ${on_string}: anchors for RNA 2 (pp)">
             <filter>'anchors-pp' in outputs</filter>
         </data>
         <data format="clustal" name="clustal"
-              label="${tool.name} chain as alignment (clustal) on ${on_string}">
+              label="${tool.name} on ${on_string}: chain as alignment (clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
         <data format="tabular" name="epm_list"
-              label="${tool.name} list of epms on ${on_string}">
+              label="${tool.name} on ${on_string}: list of epms">
             <filter>'epm_list' in outputs</filter>
         </data>
         <data format="tabular" name="chained_epm_list"
-              label="${tool.name} list of epms in chain on ${on_string}">
+              label="${tool.name} on ${on_string}: list of epms in chain">
             <filter>'chained_epm_list' in outputs</filter>
         </data>
     </outputs>
 
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="inputA" value="tRNA_2-1.fa" />
             <param name="inputB" value="tRNA_2-2.fa" />
             <param name="outputs" value="epm_list" />
             <output name="epm_list" file="tRNA_2.epms" />
+            <output name="stdout">
+                <assert_contents>
+                    <has_text text="LCSEPM preprocessing..."/>
+                    <has_text text="#EPMs:"/>
+                </assert_contents>
+            </output>
         </test>
     </tests>