--- a/macros.xml	Sat Jan 21 17:38:46 2017 -0500
+++ b/macros.xml	Mon Dec 05 13:58:16 2022 +0000
@@ -1,9 +1,12 @@
 <macros>
-    <token name="@VERSION@">1.9.0</token>
+    <token name="@TOOL_VERSION@">1.9.2.3</token>
+    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@PROFILE@">21.09</token>
 
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@VERSION@">locarna</requirement>
+            <requirement type="package" version="@TOOL_VERSION@">locarna</requirement>
+            <requirement type="package" version="4.2.2">r-base</requirement>  
         </requirements>
     </xml>
 
@@ -46,15 +49,15 @@
     </xml>
     
     <xml name="common_scoring_parameters">
-        <param name="struct_weight" argument="struct-weight"
+        <param argument="--struct-weight"
                label="Structure weight" type="integer" 
                value="200" min="0" max="800" />
-        <param name="indel_opening" argument="indel-opening"
+        <param argument="--indel-opening"
                label="Indel opening score" type="integer"
                value="-500" max="0" min="-1500" />
-        <param argument="indel" label="Indel score" type="integer" 
+        <param argument="--indel" label="Indel score" type="integer" 
                value="-350" min="-1000" max="0" />
-        <param argument="tau" type="integer" value="50"
+        <param argument="--tau" type="integer" value="50"
                min="0" max="200"
                label="Sequence contribution at structure match in percent"/> 
 
@@ -78,17 +81,17 @@
     </xml>
 
     <xml name="plfolding_parameters">
-        <param name="plfold_span" argument="--plfold-span" 
+        <param argument="--plfold-span" 
                type="integer" value="150" min="-1" max="400" 
                label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
         
-        <param name="plfold_winsize" argument="--plfold-winsize"
+        <param argument="--plfold-winsize"
                type="integer" value="300"  min="-1" max="800" 
                label="Window size for local folding" />
     </xml>
     
     <xml name="common_folding_parameters">
-        <param name="rnafold_temperature" argument="rnafold-temperature"
+        <param argument="rnafold-temperature"
                type="float" value="37.0" min="10" max="50"
                label="Temperature for RNAfold (RNAfold's -T option)" />
     </xml>
@@ -147,16 +150,18 @@
 
     </token>
 
-    <token name="@CONSTRAINT_ARGS@">
-        ## -------------------- constraint parameters
-        $Constraints.lonely_pairs
-
+    <token name="@CONSTRAINT_ARGS_WOLP@">
         #if $Constraints.maxBPspan != -1
             --maxBPspan $Constraints.maxBPspan
         #end if
 
         $Constraints.ignore_constraints
     </token>
+    <token name="@CONSTRAINT_ARGS@">
+        ## -------------------- constraint parameters
+        $Constraints.lonely_pairs
+        @CONSTRAINT_ARGS_WOLP@
+    </token>
 
     <token name="@STDOUT_ARGS@">
         $stdout_verbosity
@@ -171,7 +176,7 @@
                label="Restrict alignable positions by maximum difference" 
                help="(max-diff*)">
             <option value="off">Off</option>
-            <option value="max-diff" selected="True">Maximal difference of aligned positions</option>
+            <option value="max-diff" selected="true">Maximal difference of aligned positions</option>
             <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option> 
             <yield />
         </param>
@@ -180,12 +185,12 @@
     <xml name="max_diff_parameters_standard_cases">
         <when value="off" />
         <when value="max-diff">
-            <param  name="max_diff" argument="max-diff" type="integer"
+            <param argument="--max-diff" type="integer"
                     value="60" min="-1" max="300"
                     label="Maximal difference of aligned positions" />
         </when>
         <when value="max-diff-at-am">
-            <param  name="max_diff_at_am" argument="max-diff-at-am" type="integer" 
+            <param argument="--max-diff-at-am" type="integer" 
                     value="60" min="-1" max="300"
                     label="Maximal difference of aligned positions,
                            only at arc match positions" />
@@ -206,13 +211,13 @@
             </expand>
             <expand macro="max_diff_parameters_standard_cases" />
             <when value="max-diff-aln">
-                <param name="max_diff_aln" argument="max-diff-aln" type="data" format="clustal"
+                <param argument="--max-diff-aln" type="data" format="clustal"
                        label="Reference alignment"
                        />
-                <param  name="max_diff" argument="max-diff" type="integer"
+                <param argument="--max-diff" type="integer"
                         value="60" min="-1" max="300"
                         label="Maximal difference of aligned positions" />
-                <param name="max_diff_relax" argument="max-diff-relax" type="boolean"
+                <param argument="--max-diff-relax" type="boolean"
                        truevalue="--max-diff-relax" falsevalue=""
                        checked="False"
                        label="Relax deviation constraints in multiple
@@ -223,75 +228,79 @@
     </xml>
 
     <xml name="common_heuristic_parameters">
-        <param  name="min_prob" argument="min-prob" type="float" value="0.0005" 
+        <param argument="--min-prob" type="float" value="0.0005" 
                 min="0.0" max="0.2"
                 label="Minimal / cutoff probability" /> 
     
-        <param  name="max_diff_am" argument="max-diff-am" 
+        <param argument="--max-diff-am" 
                 type="integer" value="30" 
                 min="-1" max="300"
                 label="Maximal difference for sizes of matched arcs (-1=off)" />
         
-        <param  name="max_bps_length_ratio" argument="max-bps-length-ratio"
+        <param  argument="--max-bps-length-ratio"
                 type="float" value="0.0" min="0.0" max="10.0" 
                 label="Maximal ratio 'number of considered base pairs' by
                        'sequence length' (default: 0.0 = no effect)" />
     </xml>
     
     <xml name="common_heuristic_parameters_sparse">
-        <param  name="prob_unpaired_in_loop_threshold" argument="prob-unpaired-in-loop-threshold" type="float" value="0.00005" 
+        <param argument="--prob-unpaired-in-loop-threshold" type="float" value="0.00005" 
                 min="0.0" max="0.2"
                 label="Probability threshold for unpaired bases in loops" /> 
 
-        <param  name="prob_basepair_in_loop_threshold" argument="prob-basepair-in-loop-threshold" type="float" value="0.0001" 
+        <param argument="--prob-basepair-in-loop-threshold" type="float" value="0.0001" 
                 min="0.0" max="0.2"
                 label="Probability threshold for base pairs in loops" />       
     </xml>
     
     <xml name="in_loop_ratio_parameters">
-        <param  name="max_uil_length_ratio" argument="max-uil-length-ratio"
+        <param argument="--max-uil-length-ratio"
                 type="float" value="0.0" min="0.0" max="10.0" 
                 label="Maximal ratio 'number considered unpaired bases in loops' by
                        'sequence length' (default: 0.0; no effect)" />
         
-        <param  name="max_bpil_length_ratio" argument="max-bpil-length-ratio"
+        <param argument="--max-bpil-length-ratio"
                 type="float" value="0.0" min="0.0" max="10.0" 
                 label="Maximal ratio 'number of considered base pairs in loops'
                        by 'sequence length' (default: 0.0; no effect)" />
     </xml>
 
     <xml name="exparnap_in_loop_parameters">
-        <param  name="prob_unpaired_in_loop_threshold"
-                argument="prob_unpaired_in_loop_threshold"
+        <param argument="--prob_unpaired_in_loop_threshold"
                 type="float" value="0.01" min="0.0" max="1.0" 
                 label="Probability threshold for unpaired bases in loops" />
-        <param  name="prob_basepair_in_loop_threshold"
-                argument="prob_basepair_in_loop_threshold"
+        <param argument="--prob_basepair_in_loop_threshold"
                 type="float" value="0.01" min="0.0" max="1.0" 
                 label="Probability threshold for base pairs in loops" />
     </xml>
 
     <xml name="alifold_consensus_parameter">
-        <param  name="alifold_consensus_dp" argument="alifold-consensus-dp" 
+        <param argument="--alifold-consensus-dp" 
                 type="boolean" checked="False" 
                 truevalue="--alifold-consensus-dp" falsevalue=""
                 label="Compute consensus dot plot by alifold" />
     </xml>
     
-    <xml name="common_constraint_parameters">
-        <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" 
-               checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
-        <param name="maxBPspan" argument="--maxBPspan" 
+    <xml name="common_constraint_parameters_woLP">
+        <yield/>
+        <param argument="--maxBPspan" 
                type="integer" value="-1" min="-1" max="400" 
                label="Maximum basepair span by RNAfold; -1 for arbitrary span" />
-        <param name="ignore_constraints" argument="ignore-constraints"
+        <param argument="--ignore-constraints"
                type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""
                help="Ignore all anchor and structure constraints given
                      in the fasta(-ish) input." />
     </xml>
 
+    <xml name="common_constraint_parameters">
+        <expand macro="common_constraint_parameters_woLP">
+            <param argument="--noLP" name="lonely_pairs" type="boolean" truevalue="" falsevalue="--noLP" 
+                   checked="true" label="Allow lonely base-pairs"/>
+        </expand>
+    </xml>
+
     <xml name="standard_outupt">
-        <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
+        <data format="txt" name="stdout" label="${tool.name} on ${on_string}: stdout">
             <filter>stdout_verbosity != '--quiet'</filter>
         </data>
     </xml>
@@ -299,25 +308,25 @@
     <xml name="mlocarna_outputs">
         <expand macro="standard_outupt" />
         <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
-              label="${tool.name} alignment (annotated clustal) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (annotated clustal)">
             <filter>'clustal' in outputs</filter>
         </data>
         <data format="clustal" name="clustal_strict" 
               from_work_dir="mlocarna_results/results/result.strict-aln"
-              label="${tool.name} alignment (clustal) on ${on_string}">
-            <filter>'clustal_strict' in outputs</filter>
+              label="${tool.name} on ${on_string}: alignment (clustal)">
+            <filter>'strict' in outputs</filter>
         </data>
         <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"
-              label="${tool.name} alignment (stockholm) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (stockholm)">
             <filter>'stockholm' in outputs</filter>
         </data>
         <data format="txt" name="pp"
               from_work_dir="mlocarna_results/results/result.pp"
-              label="${tool.name} alignment (PP 2.0) on ${on_string}">
+              label="${tool.name} on ${on_string}: alignment (PP 2.0)">
             <filter>'pp' in outputs</filter>
         </data>
         <data format="tar.gz" name="mlocarna_results_tgz"
-              label="${tool.name} results archive on ${on_string}">
+              label="${tool.name} on ${on_string}: results archive">
             <filter>'mlocarna_results' in outputs</filter>
         </data>
     </xml>
@@ -330,8 +339,5 @@
             <citation type="doi">10.1186/s12859-014-0404-0</citation>
         </citations>
     </xml>
-
-
-
 </macros>