changeset 3:a1c9c960cdd5 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 94c141a71ef115279f1090f782b6f5cdeea9c277
author bgruening
date Mon, 19 Aug 2024 18:52:22 +0000
parents 535f2e41d4f7
children
files locarna_pairwise_p.xml macros.xml test-data/archaea-default.stdout test-data/archaea-probabilistic.aln test-data/archaea-ref_result.aln test-data/archaea_relplot.scr test-data/haca.snoRNA-c.aln test-data/haca.snoRNA-default.stdout test-data/haca.snoRNA.aln test-data/tRNA_2.aln test-data/tRNA_2.amprobs test-data/tRNA_2.bmprobs
diffstat 12 files changed, 450 insertions(+), 361 deletions(-) [+]
line wrap: on
line diff
--- a/locarna_pairwise_p.xml	Mon Dec 05 14:29:23 2022 +0000
+++ b/locarna_pairwise_p.xml	Mon Aug 19 18:52:22 2024 +0000
@@ -2,20 +2,14 @@
     <description>
         Partition Function and Probabilities from Pairwise Simultaneous Alignment and Folding of RNAs (LocARNA-P)
     </description>
-
     <macros>
         <import>macros.xml</import>
     </macros>
-    
     <expand macro="requirements" />
-
     <expand macro="stdio" />
-    
     <expand macro="version" />
-   
     <command><![CDATA[
     locarna_p
-
     '$inputA'
     '$inputB'
 
@@ -28,10 +22,10 @@
        --pf-scale $Heuristics.pf_scale
     #end if
 
-    ## -------------------- other parameters
+    ## -------------------- other parameters ----------------#
     @CONSTRAINT_ARGS_WOLP@
 
-    ## -------------------- probability parameters
+    ## -------------------- probability parameters ----------------#
     $Probabilities.include_am_in_bm
     #if float($Probabilities.min_bm_prob) != 0.0005
        --min-bm-prob $Probabilities.min_bm_prob
@@ -40,7 +34,7 @@
        --min-am-prob $Probabilities.min_am_prob
     #end if
 
-    ## -------------------- output
+    ## -------------------- output ----------------#
 
     #if not $arc_match_probs is None
         --write-arcmatch-probs=$arc_match_probs
@@ -55,43 +49,21 @@
     ]]></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="base_match_probs" selected="true">
-            Output base match probabilities</option>
-            <option value="arc_match_probs" selected="true">
-            Output arc match probabilities</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="base_match_probs" selected="true">Output base match probabilities</option>
+            <option value="arc_match_probs" selected="true">Output arc match probabilities</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="">Non verbose</option>
             <option value="--verbose">Verbose</option>
         </param>
-               
         <section name="Probabilities" title="Probability parameters">
-            <param argument="--include-am-in-bm"
-                   type="boolean"
-                   truevalue="--include-am-in-bm" falsevalue=""
-                   label="Include arc match cases in computation of base match probabilities" />
-            <param argument="--min-bm-prob" 
-                   type="float"
-                   value="0.0005" min="0.0" max="1.0"
-                   label="Minimal base match probability"
-                   />
-            <param argument="--min-am-prob" 
-                   type="float"
-                   value="0.0005" min="0.0" max="1.0"
-                   label="Minimal arc match probability"
-                   />                  
+            <param argument="--include-am-in-bm" type="boolean" truevalue="--include-am-in-bm" falsevalue="" label="Include arc match cases in computation of base match probabilities" />
+            <param argument="--min-bm-prob" type="float" value="0.0005" min="0.0" max="1.0" label="Minimal base match probability"/>
+            <param argument="--min-am-prob" type="float" value="0.0005" min="0.0" max="1.0" label="Minimal arc match probability"/>                  
         </section>
 
         <section name="Scoring" title="Scoring parameters">
@@ -105,16 +77,12 @@
         <section name="Heuristics" title="Heuristic parameters">
             <expand macro="common_heuristic_parameters" />
             <expand macro="max_diff_parameters_aln" />
-            <param argument="--pf-scale"
-                   type="float" value="1.0"
-                   label="Scaling of the partition function."
-                   help="Use (only) if standard scaling overflows." />
+            <param argument="--pf-scale" type="float" value="1.0" label="Scaling of the partition function." help="Use (only) if standard scaling overflows." />
         </section>
 
         <section name="Constraints" title="Constraint parameters">
             <expand macro="common_constraint_parameters_woLP" />
         </section>
-
     </inputs>
     
     <outputs>
--- a/macros.xml	Mon Dec 05 14:29:23 2022 +0000
+++ b/macros.xml	Mon Aug 19 18:52:22 2024 +0000
@@ -1,7 +1,7 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.9.2.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
-    <token name="@PROFILE@">21.09</token>
+    <token name="@TOOL_VERSION@">2.0.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
 
     <xml name="requirements">
         <requirements>
--- a/test-data/archaea-default.stdout	Mon Dec 05 14:29:23 2022 +0000
+++ b/test-data/archaea-default.stdout	Mon Aug 19 18:52:22 2024 +0000
@@ -1,9 +1,13 @@
-mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0
-Copyright Sebastian Will
-
-Compute pair probs ...
-Compute pairwise alignments ... 
-Perform progressive alignment ...
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 2.0.1
 
 
+vhuU               AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU-
+fwdB               AU-GUUGGAGGGGAACCC-GU------------AAGGGACCCUCCAAGAU-
+selD               UUACGAUGUGCCGAACCCUUU------------AAGGGAGGCACAUCGAAA
+hdrA               GG--CACCACUCGAAGGC--U------------AAGCCAAAGUGGUG-CU-
+vhuD               GU--UCUCUCGGGAACCCGUC------------AAGGGACCGAGAGA-AC-
+fruA               ---CCUCGAGGGGAACCC-GA------------AAGGGACCCGAGAGG---
+fdhA               CG-CCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGGCG-
+
 alifold            ((.(((((((((...(((.................))).))))))))))). (-31.36 = -20.01 + -11.34)
+Results written to target directory /tmp/tmpstsz4a83/job_working_directory/000/2/working/mlocarna_results.
--- a/test-data/archaea-probabilistic.aln	Mon Dec 05 14:29:23 2022 +0000
+++ b/test-data/archaea-probabilistic.aln	Mon Aug 19 18:52:22 2024 +0000
@@ -1,11 +1,10 @@
-CLUSTAL W --- LocARNA 1.9.0
-
+CLUSTAL W --- LocARNA 2.0.1
 
 
-selD               UUACGAUGUGCCGAACCCUU------------UAAGGGAGGCACAUCGAAA
-vhuU               AGC-UCACAACCGAACCCAU-------------UUGGGAGGUUGUGAG-CU
-fwdB               AUG-UUGGAGGGGAACCCGU-------------AAGGGACCCUCCAAG-AU
-hdrA               GGC-ACC-ACUCGAAGGCU--------------AAGCCAAAGU-GGUG-CU
-vhuD               GUU-CUC-UCGGGAACCCGU------------CAAGGGACCGA-GAGA-AC
-fdhA               CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUGG-CG
-fruA               CC-UCG--AGGGGAACCCGA-------------AAGGGACCC--GAGA-GG
+vhuU               AGC-UCACAACCGAACCCA-----U---U-----UGGGAGGUUGUGA-GCU
+fwdB               AUG-UUGGAGGGGAACCCG-----U---A-----AGGGACCCUCCAA-GAU
+selD               UUACGAUGUGCCGAACCCU-----U--UA-----AGGGAGGCACAUCGAAA
+hdrA               GGC-ACC-ACUCGAAGGCU---------A-----AGCCAAAGU-GGU-GCU
+vhuD               GUU-CUC-UCGGGAACCCG-----U--CA-----AGGGACCGA-GAG-AAC
+fruA               CC-UCGA--GGGGAACCCG-----A---A-----AGGGACCC--GAGA-GG
+fdhA               CGC-CACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAG-GUG-GCG
--- a/test-data/archaea-ref_result.aln	Mon Dec 05 14:29:23 2022 +0000
+++ b/test-data/archaea-ref_result.aln	Mon Aug 19 18:52:22 2024 +0000
@@ -1,5 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.0
-
+CLUSTAL W --- LocARNA 2.0.1
 
 
 vhuU               AG-CUCACAACCGAACCC-AU------------UUGGGAGGUUGUGAGCU-
--- a/test-data/archaea_relplot.scr	Mon Dec 05 14:29:23 2022 +0000
+++ b/test-data/archaea_relplot.scr	Mon Aug 19 18:52:22 2024 +0000
@@ -1,4 +1,4 @@
-pdf("/tmp/tmp5yxSuG/files/000/dataset_2.dat",width=12,height=4,version="1.4")
+pdf("/tmp/tmpewnb251n/job_working_directory/000/2/outputs/dataset_a612ea0e-aca2-4d90-987a-39141bc61f36.dat",width=12,height=4,version="1.4")
 
 rel    <- read.table("mlocarna_results/results/result.bmreliability");
 seqrel <- rel[[2]]
@@ -112,8 +112,8 @@
 
 if (0!=1) {
 
-  on  <- c(0,4,33,44,49);
-  off <- c(3,20,43,48,51);
+  on  <- c(0,33);
+  off <- c(20,51);
 
   if (length(on)>0) {
     for (i in 1:length(on)) {
@@ -123,8 +123,8 @@
 
   ### draw on/off values
   if (0) {
-    lines(c(1,1+len),c(0.0355791,0.0355791),lty=2,lwd=1)
-    lines(c(1,1+len),c(0.702675,0.702675),lty=2,lwd=1)
+    lines(c(1,1+len),c(0.0139513,0.0139513),lty=2,lwd=1)
+    lines(c(1,1+len),c(0.656017,0.656017),lty=2,lwd=1)
   }
 }
 
--- a/test-data/haca.snoRNA-c.aln	Mon Dec 05 14:29:23 2022 +0000
+++ b/test-data/haca.snoRNA-c.aln	Mon Aug 19 18:52:22 2024 +0000
@@ -1,4 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.2.3
+CLUSTAL W --- LocARNA 2.0.1
 
 ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
 ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
--- a/test-data/haca.snoRNA-default.stdout	Mon Dec 05 14:29:23 2022 +0000
+++ b/test-data/haca.snoRNA-default.stdout	Mon Aug 19 18:52:22 2024 +0000
@@ -1,10 +1,20 @@
-mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0
-Copyright Sebastian Will
-
-Compute pair probs ...
-Compute pairwise alignments ... 
-Perform progressive alignment ...
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 2.0.1
 
 
-alifold            .((((((((........((((.(((((((......))))))).))))......))..)))))).............(((((((...((......((((((((((((.....)))))))))
-                   ))).........)).))).))))......... (-62.29 = -34.50 + -27.79)
+ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30              UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
+ACA5               UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGCUGCCACAGAAACAC--UGUGAC-----UCAUG-GGCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59              GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG--CCCAUGGGUGA-CCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+#A1                ................................................................AAAAAA..................................................
+#A2                ................................................................123456..................................................
+
+ACA7               AUUGGA-----AGACACU-CUGCG-----ACA
+ACA30              CAACUG-----UCACUCA-AUGGG-----ACA
+ACA5               GGAUAA-----AUUUGGU-UACAG-----ACA
+ACA59              ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+#A1                .............................BBB
+#A2                .............................123
+
+alifold            .((((((..........((((..(((((........)))))..))))..........)))))).............((((((.............((((((((..........)))).))
+                   ))..............)).))))......... (-53.08 = -26.63 + -26.46)
+Results written to target directory /tmp/tmpstsz4a83/job_working_directory/000/4/working/mlocarna_results.
--- a/test-data/haca.snoRNA.aln	Mon Dec 05 14:29:23 2022 +0000
+++ b/test-data/haca.snoRNA.aln	Mon Aug 19 18:52:22 2024 +0000
@@ -1,4 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.2.3
+CLUSTAL W --- LocARNA 2.0.1
 
 ACA7               ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUU-CGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUC-CAUUCCCAGCUUGCUCCGUAGCUGGCG
 ACA30              UGGCACUUU--CACAGUUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAAC---CC-UUG--AUUGUAUU-CUUGCCCUGGG---AUUAUACCAGUGG
--- a/test-data/tRNA_2.aln	Mon Dec 05 14:29:23 2022 +0000
+++ b/test-data/tRNA_2.aln	Mon Aug 19 18:52:22 2024 +0000
@@ -1,4 +1,4 @@
-CLUSTAL W --- LocARNA 1.9.2.3 --- Score: 2587
+CLUSTAL W --- LocARNA 2.0.1 --- Score: 2587
 
 D10744             GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
 AF008220           GGAGGAUUAGC--UCAGCUGGGAGAGCAUCUGCCUUA-------CAAGCAGAGGGUCGGCG-GUUCGAGCCCGUCAUCCUCCA
--- a/test-data/tRNA_2.amprobs	Mon Dec 05 14:29:23 2022 +0000
+++ b/test-data/tRNA_2.amprobs	Mon Aug 19 18:52:22 2024 +0000
@@ -1,108 +1,185 @@
-64 69 54 59 0.079977
-63 70 53 60 0.0158884
-63 71 53 61 0.0915855
-62 72 52 62 0.203921
-61 73 51 63 0.202155
-60 74 50 64 0.175676
-59 75 49 65 0.0815626
-39 44 33 38 0.0114647
-39 46 33 37 0.0168669
-38 47 33 38 0.0303705
-37 48 32 39 0.0111801
-37 48 31 39 0.0434528
-36 42 34 38 0.0105213
-36 42 33 37 0.0442772
-36 42 33 38 0.0150469
-36 49 30 40 0.0445378
-35 40 33 37 0.0438048
-35 40 33 38 0.0131652
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-34 44 32 39 0.0318614
-34 44 31 39 0.0265932
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-33 42 31 39 0.123358
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--- a/test-data/tRNA_2.bmprobs	Mon Dec 05 14:29:23 2022 +0000
+++ b/test-data/tRNA_2.bmprobs	Mon Aug 19 18:52:22 2024 +0000
@@ -1,172 +1,204 @@
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