From 5a2a8b956092702f56a937cb632c5792cc291e60 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 16 Nov 2022 21:42:31 +0100
Subject: [PATCH] add missing parameters to command

or remove non existent parameters from inputs

xref https://github.com/bgruening/galaxytools/issues/1185
---
 tools/rna_tools/locarna/locarna_exparnap.xml  |  4 ++-
 tools/rna_tools/locarna/locarna_multiple.xml  |  1 -
 .../rna_tools/locarna/locarna_pairwise_p.xml  | 23 ++++-------------
 tools/rna_tools/locarna/macros.xml            | 25 +++++++++++--------
 .../locarna/test-data/haca.snoRNA-c.aln       | 16 ++++++------
 .../locarna/test-data/haca.snoRNA.aln         | 16 ++++++------
 tools/rna_tools/locarna/test-data/tRNA_2.aln  |  6 ++---
 tools/rna_tools/locarna/test-data/tRNA_2.epms |  2 +-
 8 files changed, 43 insertions(+), 50 deletions(-)

diff --git a/tools/rna_tools/locarna/locarna_exparnap.xml b/tools/rna_tools/locarna/locarna_exparnap.xml
index b06a6b8912..56f6f9c01e 100644
--- a/tools/rna_tools/locarna/locarna_exparnap.xml
+++ b/tools/rna_tools/locarna/locarna_exparnap.xml
@@ -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($Other.subopt.subopt_selector) == "on"
diff --git a/tools/rna_tools/locarna/locarna_multiple.xml b/tools/rna_tools/locarna/locarna_multiple.xml
index 424db0f1e0..8234d13ba0 100644
--- a/tools/rna_tools/locarna/locarna_multiple.xml
+++ b/tools/rna_tools/locarna/locarna_multiple.xml
@@ -69,7 +69,6 @@
     #if 'clustal_strict' in str($outputs).split(",")
         && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
     #end if
-    && echo $outputs
     ]]></command>
 
     <inputs>
diff --git a/tools/rna_tools/locarna/locarna_pairwise_p.xml b/tools/rna_tools/locarna/locarna_pairwise_p.xml
index 9330380f53..0adace6ad8 100644
--- a/tools/rna_tools/locarna/locarna_pairwise_p.xml
+++ b/tools/rna_tools/locarna/locarna_pairwise_p.xml
@@ -15,12 +15,12 @@
    
     <command><![CDATA[
     locarna_p
-    
+
     '$inputA'
     '$inputB'
-    
+
     @SCORING_ARGS@
-    
+
     @FOLDING_ARGS@
 
     @HEURISTIC_ARGS@
@@ -29,12 +29,7 @@
     #end if
 
     ## -------------------- other parameters
-        
-    #if $Constraints.maxBPspan != -1
-        --maxBPspan $Constraints.maxBPspan
-    #end if
-
-    $Constraints.ignore_constraints
+    @CONSTRAINT_ARGS_WOLP@
 
     ## -------------------- probability parameters
     $Probabilities.include_am_in_bm
@@ -105,14 +100,6 @@
         
         <section name="Folding" title="RNA folding parameters">
             <expand macro="common_folding_parameters" />
-            <expand macro="alifold_consensus_parameter" />
-            <param name="consensus_structure" type="select" label="Consensus structure type"
-                   help="Type of consensus structures written to screen and stockholm output"
-                   >
-                <!-- <option value="mea">mea</option>-->
-                <option value="none">none</option>
-                <option value="alifold">alifold</option>
-            </param>
         </section>
 
         <section name="Heuristics" title="Heuristic parameters">
@@ -125,7 +112,7 @@
         </section>
 
         <section name="Constraints" title="Constraint parameters">
-            <expand macro="common_constraint_parameters" />
+            <expand macro="common_constraint_parameters_woLP" />
         </section>
 
     </inputs>
diff --git a/tools/rna_tools/locarna/macros.xml b/tools/rna_tools/locarna/macros.xml
index 9f27381e8e..4fb78b0413 100644
--- a/tools/rna_tools/locarna/macros.xml
+++ b/tools/rna_tools/locarna/macros.xml
@@ -149,16 +149,18 @@
 
     </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
@@ -278,9 +280,8 @@
                 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)" />
+    <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" />
@@ -290,6 +291,13 @@
                      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} on ${on_string}: stdout">
             <filter>stdout_verbosity != '--quiet'</filter>
@@ -330,8 +338,5 @@
             <citation type="doi">10.1186/s12859-014-0404-0</citation>
         </citations>
     </xml>
-
-
-
 </macros>
 
diff --git a/tools/rna_tools/locarna/test-data/haca.snoRNA-c.aln b/tools/rna_tools/locarna/test-data/haca.snoRNA-c.aln
index 614c09cc66..992477fce2 100644
--- a/tools/rna_tools/locarna/test-data/haca.snoRNA-c.aln
+++ b/tools/rna_tools/locarna/test-data/haca.snoRNA-c.aln
@@ -1,15 +1,15 @@
-CLUSTAL W --- LocARNA 1.9.0
+CLUSTAL W --- LocARNA 1.9.2.3
 
-ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
-ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
-ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
-ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
+ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGACUCAUGG------GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGC-UGGCCCAUG--GGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
 #A1                ................................................................AAAAAA..................................................
 #A2                ................................................................123456..................................................
 
-ACA7               AUUGGA--AGA---CACU-CUGCG-----ACA
-ACA30              CAACUG--UCA---CUCA-AUGGG-----ACA
-ACA5               GGAUAA--AUU---UGGU-UACAG-----ACA
+ACA7               AUUGGAA-----GACACUC-UGC-----GACA
+ACA30              CAACUGU-----CACUCAA-UGG-----GACA
+ACA5               GGAUAAA-----UUUGGUU-ACA-----GACA
 ACA59              ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
 #A1                .............................BBB
 #A2                .............................123
diff --git a/tools/rna_tools/locarna/test-data/haca.snoRNA.aln b/tools/rna_tools/locarna/test-data/haca.snoRNA.aln
index 0d38163e35..a26541c6bf 100644
--- a/tools/rna_tools/locarna/test-data/haca.snoRNA.aln
+++ b/tools/rna_tools/locarna/test-data/haca.snoRNA.aln
@@ -1,11 +1,11 @@
-CLUSTAL W --- LocARNA 1.9.0
+CLUSTAL W --- LocARNA 1.9.2.3
 
-ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
-ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
-ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
-ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUG--GGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
+ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGC--CCAGAAGGCUGCCACAGAAACAC--UGUGACUCAUGG------GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGC-UGGCCCAUG--GGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
 
-ACA7               AUUGGA--AGA---CACU-CUGCG-----ACA
-ACA30              CAACUG--UCA---CUCA-AUGGG-----ACA
-ACA5               GGAUAA--AUU---UGGU-UACAG-----ACA
+ACA7               AUUGGAA-----GACACUC-UGC-----GACA
+ACA30              CAACUGU-----CACUCAA-UGG-----GACA
+ACA5               GGAUAAA-----UUUGGUU-ACA-----GACA
 ACA59              ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
diff --git a/tools/rna_tools/locarna/test-data/tRNA_2.aln b/tools/rna_tools/locarna/test-data/tRNA_2.aln
index c1b8a595bd..2b70024c8e 100644
--- a/tools/rna_tools/locarna/test-data/tRNA_2.aln
+++ b/tools/rna_tools/locarna/test-data/tRNA_2.aln
@@ -1,4 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.0 --- Score: 2875
+CLUSTAL W --- LocARNA 1.9.2.3 --- Score: 2587
 
-D10744             GGAAAAUU-GAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
-AF008220           GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGG-----------UCGGCGGUUCGAGCCCGUCAUCCUCCA
+D10744             GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
+AF008220           GGAGGAUUAGC--UCAGCUGGGAGAGCAUCUGCCUUA-------CAAGCAGAGGGUCGGCG-GUUCGAGCCCGUCAUCCUCCA
diff --git a/tools/rna_tools/locarna/test-data/tRNA_2.epms b/tools/rna_tools/locarna/test-data/tRNA_2.epms
index e45fa0fa11..626f19d90d 100644
--- a/tools/rna_tools/locarna/test-data/tRNA_2.epms
+++ b/tools/rna_tools/locarna/test-data/tRNA_2.epms
@@ -1,4 +1,4 @@
 epm_id	 score	 structure	 positions
-0	3583	((()))	1:4 2:5 3:6 80:67 81:68 82:69 
+0	3587	((()))	1:4 2:5 3:6 80:67 81:68 82:69 
 1	3593	((()))	1:1 2:2 3:3 80:70 81:71 82:72