--- a/locarna_exparnap.xml	Mon Dec 05 13:58:16 2022 +0000
+++ b/locarna_exparnap.xml	Mon Aug 19 18:53:00 2024 +0000
@@ -2,25 +2,18 @@
     <description>
         Pairwise Simultaneous Matching and Folding of RNAs (ExpaRNA-P)
     </description>
-
     <macros>
         <import>macros.xml</import>
     </macros>
-
-    <expand macro="requirements" />
-
-    <expand macro="stdio" />
-
-    <expand macro="version" />
-
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version"/>
     <command><![CDATA[
     exparna_p
-
     '$inputA'
     '$inputB'
 
-    ## -------------------- scoring parameters
-    #
+    ## -------------------- scoring parameters -------------#
     $Scoring.no_stacking
     --alpha_1 $Scoring.alpha_1
     --alpha_2 $Scoring.alpha_2
@@ -35,8 +28,7 @@
 
     @CONSTRAINT_ARGS@
     @FOLDING_ARGS@
-    ## -------------------- other parameters
-    #
+    ## -------------------- other parameters---------------- #
     #if str($Other.subopt.subopt_selector) == "on"
         --diff-to-opt-score $Other.subopt.diff_to_opt_score
         --number-of-EPMs $Other.subopt.number_of_EPMs
@@ -49,7 +41,7 @@
     $Other.no_chaining
     --out-min-prob $Other.out_min_prob
 
-    ## -------------------- output
+    ## -------------------- output ---------------- #
 
     #if 'postscript' in str($outputs).split(",")
         --output-ps
@@ -79,7 +71,7 @@
 
     @STDOUT_ARGS@
 
-    ## -------------------- post processing
+    ## -------------------- post processing --------------#
 
     #if 'anchors-pp' in str($outputs).split(",")
         && mv anchors_pp_A.pp '$anchors_ppA'
@@ -89,161 +81,95 @@
     ]]></command>
 
     <inputs>
-        <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A"
-               help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"
-               />
-        <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B"
-               help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"
-               />
-
-        <param name="outputs" type="select" display="checkboxes" multiple="true"
-               label="Output options">
-            <option value="postscript" selected="false">Best EPM chain
-            as colored postscript</option>
-            <option value="anchors-fasta" selected="false">Fasta with anchor
-            constraints from chaining</option>
-            <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
-            alignment in Clustal format</option>
+        <param name="inputA" type="data" format="fasta,clustal,txt" label="Sequence A" help="First sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
+        <param name="inputB" type="data" format="fasta,clustal,txt" label="Sequence B" help="Second sequence in fasta, clustal, dp_ps, or PP2.0 format"/>
+        <param name="outputs" type="select" display="checkboxes" multiple="true" label="Output options">
+            <option value="postscript" selected="false">Best EPM chain as colored postscript</option>
+            <option value="anchors-fasta" selected="false">Fasta with anchor constraints from chaining</option>
+            <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 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
-            EPMs in the best chain</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="--quiet">Don't report standard output</option>
             <option value="" selected="true">Non verbose</option>
             <option value="--verbose">Verbose</option>
         </param>
-
         <section name="Scoring" title="Scoring parameters">
-            <param argument="--alpha_1"
-                   type="integer" value="1" min="0" max="50"
-                   label="Sequence score factor"
-                   />
-            <param argument="--alpha_2"
-                   type="integer" value="5" min="0" max="50"
-                   label="Structure score factor"
-                   />
-            <param argument="--no-stacking" type="boolean"
-                   truevalue="" falsevalue="--no-stacking"
-                   label="Add stacking terms"
-                   />
-            <param argument="--alpha_3"
-                   type="integer" value="5" min="0" max="50"
-                   label="Stacking score factor"
-                   />
-            <param argument="--struct-mismatch-score"
-                   type="integer" value="-10" min="-100" max="0"
-                   label="Score for nucleotide mismatch in base pair match"
-                   />
+            <param argument="--alpha_1" type="integer" value="1" min="0" max="50" label="Sequence score factor"/>
+            <param argument="--alpha_2" type="integer" value="5" min="0" max="50" label="Structure score factor"/>
+            <param argument="--no-stacking" type="boolean" truevalue="" falsevalue="--no-stacking" label="Add stacking terms"/>
+            <param argument="--alpha_3" type="integer" value="5" min="0" max="50" label="Stacking score factor"/>
+            <param argument="--struct-mismatch-score" type="integer" value="-10" min="-100" max="0" label="Score for nucleotide mismatch in base pair match"/>
         </section>
-
         <section name="Folding" title="RNA folding parameters">
             <expand macro="common_folding_parameters" />
         </section>
-
         <section name="Heuristics" title="Heuristic parameters">
             <expand macro="common_heuristic_parameters" />
             <expand macro="max_diff_parameters" />
             <expand macro="in_loop_ratio_parameters" />
             <expand macro="exparnap_in_loop_parameters" />
         </section>
-
         <section name="Constraints" title="Constraint parameters">
             <expand macro="common_constraint_parameters" />
         </section>
-
-
         <section name="Other" title="Other parameters">
             <conditional name="subopt">
-                <param name="subopt_selector" type="select"
-                       label="Suboptimal traceback of EPMs (exact pattern matches)"
-                       help="(--subopt)">
-                    <option value="off">Enumerate only optimal
-                    EPMs</option>
+                <param name="subopt_selector" type="select" label="Suboptimal traceback of EPMs (exact pattern matches)" help="(--subopt)">
+                    <option value="off">Enumerate only optimal EPMs</option>
                     <option value="on">Perform suboptimal traceback of EPMs</option>
                 </param>
                 <when value="off" />
                 <when value="on">
-                    <param argument="--diff-to-opt-score"
-                           type="integer" value="-1" min="-20" max="0"
-                           label="Maximum score difference to optimum" />
-                    <param argument="--number-of-EPMs"
-                           type="integer" value="100" min="1" max="10000"
-                           label="Maximal number of EPMs" />
+                    <param argument="--diff-to-opt-score" type="integer" value="-1" min="-20" max="0" label="Maximum score difference to optimum" />
+                    <param argument="--number-of-EPMs" type="integer" value="100" min="1" max="10000" label="Maximal number of EPMs" />
                 </when>
             </conditional>
 
-            <param argument="--min-score"
-                   type="integer" value="30" min="0" max="1000"
-                   label="Minimum score of EPM" />
-
-            <param argument="--inexact-struct-match" type="boolean"
-                   truevalue="--inexact-struct-match" falsevalue=""
-                   label="Allow inexact structure matches"/>
-
-            <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 argument="--no-chaining" type="boolean"
-                   truevalue="" falsevalue="--no-chaining" checked="true"
-                   label="Find best overall chain by chaining"/>
-
-            <param argument="--out-min-prob"
-                   type="float" value="0.0005" min="0" max="1"
-                   label="Minimal probability in output (min-prob overrides if smaller)"/>
-
+            <param argument="--min-score" type="integer" value="30" min="0" max="1000" label="Minimum score of EPM" />
+            <param argument="--inexact-struct-match" type="boolean" truevalue="--inexact-struct-match" falsevalue="" label="Allow inexact structure matches"/>
+            <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 argument="--no-chaining" type="boolean" truevalue="" falsevalue="--no-chaining" checked="true" label="Find best overall chain by chaining"/>
+            <param argument="--out-min-prob" type="float" value="0.0005" min="0" max="1" label="Minimal probability in output (min-prob overrides if smaller)"/>
         </section>
     </inputs>
 
     <outputs>
         <expand macro="standard_outupt" />
-        <data format="ps" name="ps_fileA"
-              label="${tool.name} on ${on_string}: chain in RNA 1 (postscript)">
+        <data format="ps" name="ps_fileA" label="${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} on ${on_string}: chain in RNA 2 (postscript)">
+        <data format="ps" name="ps_fileB" label="${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} on ${on_string}: anchor constraints from chain (fasta)">
+        <data format="txt" name="anchors_fasta" label="${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} on ${on_string}: anchors for RNA 1 (pp)">
+        <data format="txt" name="anchors_ppA" label="${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} on ${on_string}: anchors for RNA 2 (pp)">
+        <data format="txt" name="anchors_ppB" label="${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} on ${on_string}: chain as alignment (clustal)">
+        <data format="clustal" name="clustal" label="${tool.name} on ${on_string}: chain as alignment (clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
-        <data format="tabular" name="epm_list"
-              label="${tool.name} on ${on_string}: list of epms">
+        <data format="tabular" name="epm_list" label="${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} on ${on_string}: list of epms in chain">
+        <data format="tabular" name="chained_epm_list" label="${tool.name} on ${on_string}: list of epms in chain">
             <filter>'chained_epm_list' in outputs</filter>
         </data>
     </outputs>
 
     <tests>
         <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" />
+            <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..."/>