# HG changeset patch
# User rnateam
# Date 1482969134 18000
# Node ID 8414fea2a6fd57ea4270e3441fec978ad3bf23c2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 1d1d9aac8cb96d043be07f2e4059baa3b05c2afc
diff -r 000000000000 -r 8414fea2a6fd locarna.tar.bz2
Binary file locarna.tar.bz2 has changed
diff -r 000000000000 -r 8414fea2a6fd locarna_multiple.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/locarna_multiple.xml Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,311 @@
+
+
+ Multiple Alignment and Folding of RNAs
+
+
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+ macros.xml
+
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+
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+
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+ =0
+ --plfold-span $Folding.plfold_span
+ --plfold-winsize $Folding.plfold_winsize
+ #end if
+
+ #if float($Folding.rnafold_temperature) != 37.0
+ --rnafold-temperature $Folding.rnafold_temperature
+ #end if
+
+ $Folding.alifold_consensus_dp
+
+ ## -------------------- heuristic parameters
+
+ -p $Heuristics.min_prob
+ --max-diff-am $Heuristics.max_diff_am
+ --max-diff $Heuristics.max_diff
+ --max-diff-at-am $Heuristics.max_diff_at_am
+ --max-bps-length-ratio $Heuristics.max_bps_length_ratio
+
+
+ ## -------------------- other parameters
+
+ #if str($Constraint.bed_anchors.bed_anchors_selector) == "yes"
+ --anchor-constraints $Constraint.bed_anchors.bed_anchors_file
+ #end if
+
+ $Constraint.lonely_pairs
+
+ #if $Constraint.maxBPspan != -1
+ --maxBPspan $Constraint.maxBPspan
+ #end if
+
+ $Constraint.ignore_constraints
+
+ $stdout_verbosity
+
+ #if str($stdout_verbosity) != "--quiet":
+ > '$stdout'
+ #end if
+
+ #if 'clustal_strict' in str($outputs).split(",")
+ && grep -v '^#' mlocarna_results/results/result.aln > mlocarna_results/results/result.strict-aln
+ #end if
+
+ ]]>
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+ fruA
+ CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG
+ >fdhA
+ CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG
+ >vhuU
+ AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU
+
+Morover, mlocarna supports structure constraints for folding and anchor
+constraints for alignment. Both types of constraints can be specified
+in extension of the standard fasta format via 'constraint
+lines'. Fasta-ish input with constraints looks like this::
+
+ >A
+ GACCCUGGGAACAUUAACUACUCUCGUUGGUGAUAAGGAACA
+ ..((.(....xxxxxx...................))).xxx #S
+ ..........000000.......................111 #1
+ ..........123456.......................123 #2
+ >B
+ ACGGAGGGAAAGCAAGCCUUCUGCGACA
+ .(((....xxxxxx.......))).xxx #S
+ ........000000...........111 #1
+ ........123456...........123 #2
+
+The same anchor constraints (like by the lines tagged #1, #2) can
+alternatively be specified in bed format by the entries::
+
+ A 10 16 first_box
+ B 8 14 first_box
+ A 39 42 ACA-box
+ B 25 28 ACA-box
+
+where anchor regions (boxes) have arbitrary but matching names
+and contig/sequence names correspond to the sequence names
+of the fasta(-like) input.
+
+
+**Output.**
+
+The final alignment is reported in standard and/or variants of the
+clustal and stockholm format. Moreover, an archive with final and
+intermediary results of the mlocarna run can be returned.
+
+
+For more information, see
+.. __: http://www.bioinf.uni-freiburg.de/Software/LocARNA/
+ ]]>
+
+
+
+
diff -r 000000000000 -r 8414fea2a6fd macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,178 @@
+
+ 1.9.0
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+ locarna
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+ stdout_verbosity != '--quiet'
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+ 'clustal' in outputs
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+ 'clustal_strict' in outputs
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+ 'stockholm' in outputs
+
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+ 'pp' in outputs
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+ 'mlocarna_results' in outputs
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+
+
+ 10.1371/journal.pcbi.0030065
+ 10.1261/rna.029041.111
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diff -r 000000000000 -r 8414fea2a6fd test-data/archaea-default.stdout
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-default.stdout Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,18 @@
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0
+Copyright Sebastian Will
+
+Compute pair probs ...
+Compute pairwise alignments ...
+Perform progressive alignment ...
+
+
+
+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 ((.(((((((((...(((.................))).))))))))))). (-31.59 = -20.01 + -11.58)
diff -r 000000000000 -r 8414fea2a6fd test-data/archaea-probabilistic.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea-probabilistic.aln Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,11 @@
+CLUSTAL W --- LocARNA 1.9.0
+
+
+
+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
diff -r 000000000000 -r 8414fea2a6fd test-data/archaea.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea.fa Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,14 @@
+>fruA
+CCUCGAGGGGAACCCGAAAGGGACCCGAGAGG
+>fdhA
+CGCCACCCUGCGAACCCAAUAUAAAAUAAUACAAGGGAGCAGGUGGCG
+>vhuU
+AGCUCACAACCGAACCCAUUUGGGAGGUUGUGAGCU
+>hdrA
+GGCACCACUCGAAGGCUAAGCCAAAGUGGUGCU
+>vhuD
+GUUCUCUCGGGAACCCGUCAAGGGACCGAGAGAAC
+>selD
+UUACGAUGUGCCGAACCCUUUAAGGGAGGCACAUCGAAA
+>fwdB
+AUGUUGGAGGGGAACCCGUAAGGGACCCUCCAAGAU
diff -r 000000000000 -r 8414fea2a6fd test-data/archaea.tar.gz
Binary file test-data/archaea.tar.gz has changed
diff -r 000000000000 -r 8414fea2a6fd test-data/archaea_relplot.scr
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/archaea_relplot.scr Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,137 @@
+pdf("/tmp/tmp5yxSuG/files/000/dataset_2.dat",width=12,height=4,version="1.4")
+
+rel <- read.table("mlocarna_results/results/result.bmreliability");
+seqrel <- rel[[2]]
+strrel <- rel[[3]]
+
+if ("" != "") {
+ seq <- ""
+ seq <- strsplit(seq,split="")
+ tab <- unlist(seq)!="-"
+
+ seqrel<-seqrel[tab]
+ strrel<-strrel[tab]
+}
+
+len<-length(seqrel)
+
+if (0) {
+ seqrel<-seqrel[len:1]
+ strrel<-strrel[len:1]
+}
+
+
+
+if (1) {
+ seqrel <- seqrel/1.0
+}
+
+
+totalrel <- seqrel+strrel;
+
+anno_space<-0.075
+
+maxy <- max(c(1,totalrel))+anno_space*(0+1);
+
+
+firstpos <- 1
+lastpos <- 1+len-1
+
+if (0) {
+ the_xlim <- c(lastpos,firstpos)
+} else {
+ the_xlim <- c(firstpos,lastpos)
+}
+
+# set margin
+# b, l, t, r
+par(mar=c(6,2.5,1,1))
+
+# open plot (and draw threshold)
+plot(c(0),c(0),type="l",
+ xlab="",ylab="",
+ xlim=the_xlim,ylim=c(0,maxy),
+ yaxp=c(0,1,2))
+
+## title inside of plot
+legend("topleft","",bty="n")
+
+
+# total reliability
+polygon(c(firstpos,firstpos:lastpos,lastpos),c(0,totalrel,0),col=rgb(0.8,0.8,0.9,0.5),lwd=2,border=FALSE)
+lines(firstpos:lastpos,totalrel,col="blue",lwd=2)
+
+# plot structure reliability
+polygon(c(firstpos,firstpos:lastpos,lastpos),c(0,strrel,0),col=rgb(0.3,0.3,0.5,0.8),lwd=1,border=FALSE)
+
+
+## draw other signals
+signals<-c();
+signal_sizes<-c();
+
+signal_starts <- 1:0
+
+signal_starts[1]<-1;
+if (0>1) {
+ for (i in 2:0) {
+ signal_starts[i]<-signal_starts[i-1]+signal_sizes[i-1]*2+1;
+ }
+}
+
+colors <- c(
+ rgb(0.6,0.1,0.1,0.9),
+ rgb(0.6,0.6,0.1,0.9),
+ rgb(0.1,0.6,0.6,0.9),
+ rgb(0.6,0.1,0.6,0.9)
+);
+colors<-c(colors,colors);
+
+if (0>0) {
+
+ for (i in 1:0) {
+ orientation <- signals[signal_starts[i]+signal_sizes[i]*2];
+ sig_y <- maxy-i*anno_space;
+
+ for (j in 0:(signal_sizes[i]-1)) {
+
+ sig_x <- c(signals[signal_starts[i]+j*2],signals[signal_starts[i]+j*2+1]);
+
+ ## draw arrows
+ if (orientation!=0) {
+ the_code <- 1+(orientation+1)/2;
+ arrows(sig_x[1],sig_y,sig_x[2],sig_y,lwd=4,col=colors[i],code=the_code,angle=20,length=0.15);
+ } else {
+ lines(sig_x,c(sig_y,sig_y),lwd=4,col=colors[i]);
+ }
+ }
+ }
+}
+
+#draw inferred on-signal
+hit_color <- rgb(0.1,0.6,0.1,0.9)
+
+if (0!=1) {
+
+ on <- c(0,4,33,44,49);
+ off <- c(3,20,43,48,51);
+
+ if (length(on)>0) {
+ for (i in 1:length(on)) {
+ lines(c(1+on[i],1+off[i]-1),c(maxy,maxy),lwd=7,col=hit_color);
+ }
+ }
+
+ ### 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)
+ }
+}
+
+
+signal_names<-c();
+
+if (length(signal_names)>0 || (0!=1)) {
+ legend("bottom",c("LocARNA",signal_names),lwd=7,col=c(hit_color,colors),horiz=TRUE,inset=-0.4);
+ # ,xpd=TRUE
+}
diff -r 000000000000 -r 8414fea2a6fd test-data/haca.snoRNA-default.stdout
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA-default.stdout Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,33 @@
+mLocARNA --- multiple Local (and global) Alignment of RNA --- LocARNA 1.9.0
+Copyright Sebastian Will
+
+Compute pair probs ...
+Compute pairwise alignments ...
+Perform progressive alignment ...
+
+
+
+ACA7 ACCUCCUGGGAUCGCAUCUGG-AGAGUGC---CUAGUAUUCUGCCAGCUUCGGAA-AGGG
+ACA30 UGGCACUUUCACAG--UUCCU-UCCCCAG---GCAGUGGGGCCAGGAUUUGGUAGCUGGU
+ACA5 UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAA--GGC
+ACA59 GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGG-CCCAUGGGUGAC--CCU
+#A1 ............................................................
+#A2 ............................................................
+
+ACA7 AGGGAAAGCAAGCCUGGCAGAG-GCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCG
+ACA30 GCUGAGAGAAAAC---CC-UUG---AUUGUAUUCUUGCCCUGGG---AUUAUACCAGUGG
+ACA5 UGCCACAGAAACAC--UGUGAC-UCAUGG-----GCCCUGUUCCUGUGUCCCAGGCUCAG
+ACA59 GGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUA
+#A1 ....AAAAAA..................................................
+#A2 ....123456..................................................
+
+ACA7 AUUGGA--AGA---CACU-CUGCG-----ACA
+ACA30 CAACUG--UCA---CUCA-AUGGG-----ACA
+ACA5 GGAUAA--AUU---UGGU-UACAG-----ACA
+ACA59 ACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+#A1 .............................BBB
+#A2 .............................123
+
+alifold .((((((((........((((.(((((((......))))))).))))......))..)))
+ ))).............((((((.....((.....((((((((((((.....)))))))))
+ )))......)).....)).))))......... (-61.69 = -33.85 + -27.84)
diff -r 000000000000 -r 8414fea2a6fd test-data/haca.snoRNA.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA.fa Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,21 @@
+>ACA59
+GCCCAGGGUAUGUUCACGGGGCGAUGCUGCCCUCCCAGCUGGCCCAUGGGUGACCCUGGGAACAUUAACUGCCUCACAACGUUUGUGCCUCAGUUACCCGUAGAUGUAGUGAGGGUAACAAUACUUACUCUCGUUGGUGAUAAGGAACA
+.............................................................xxxxxx...............................................................................xxx #S
+.............................................................AAAAAA...............................................................................BBB #1
+.............................................................123456...............................................................................123 #2
+
+>ACA7
+ACCUCCUGGGAUCGCAUCUGGAGAGUGCCUAGUAUUCUGCCAGCUUCGGAAAGGGAGGGAAAGCAAGCCUGGCAGAGGCACCCAUUCCAUUCCCAGCUUGCUCCGUAGCUGGCGAUUGGAAGACACUCUGCGACA
+...........................................................xxxxxx...................................................................xxx #S
+...........................................................AAAAAA...................................................................BBB #1
+...........................................................123456...................................................................123 #2
+>ACA5
+UGCAGCCGUGUCAAAUUCAGUACCUGUCCUAUGCAUGGUAGGCACUGGCCCAGAAGGCUGCCACAGAAACACUGUGACUCAUGGGCCCUGUUCCUGUGUCCCAGGCUCAGGGAUAAAUUUGGUUACAGACA
+..............................................................xxxxxx............................................................xxx #S
+..............................................................AAAAAA............................................................BBB #1
+..............................................................123456............................................................123 #2
+>ACA30
+UGGCACUUUCACAGUUCCUUCCCCAGGCAGUGGGGCCAGGAUUUGGUAGCUGGUGCUGAGAGAAAACCCUUGAUUGUAUUCUUGCCCUGGGAUUAUACCAGUGGCAACUGUCACUCAAUGGGACA
+..........................................................xxxxxx..........................................................xxx #S
+..........................................................AAAAAA..........................................................BBB #1
+..........................................................123456..........................................................123 #2
diff -r 000000000000 -r 8414fea2a6fd test-data/haca.snoRNA_anchor.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/haca.snoRNA_anchor.bed Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,8 @@
+ACA59 61 67 ANANNA
+ACA7 59 65 ANANNA
+ACA5 62 68 ANANNA
+ACA30 58 64 ANANNA
+ACA59 146 149 ACA
+ACA7 132 135 ACA
+ACA5 128 131 ACA
+ACA30 122 125 ACA
diff -r 000000000000 -r 8414fea2a6fd test-data/tRNA_2-1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2-1.fa Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,2 @@
+>D10744
+GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
diff -r 000000000000 -r 8414fea2a6fd test-data/tRNA_2-2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2-2.fa Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,2 @@
+>AF008220
+GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA
diff -r 000000000000 -r 8414fea2a6fd test-data/tRNA_2.aln
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_2.aln Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,7 @@
+CLUSTAL W --- LocARNA 1.9.0 --- Score: 2875
+
+D10744 GGAAAAUU-GAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGG
+AF008220 GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGG-----------UCG
+
+D10744 UGAGUUCGAAUCUCACAUUUUCCG
+AF008220 GCGGUUCGAGCCCGUCAUCCUCCA
diff -r 000000000000 -r 8414fea2a6fd test-data/tRNA_5.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tRNA_5.fa Wed Dec 28 18:52:14 2016 -0500
@@ -0,0 +1,10 @@
+>D10744
+GGAAAAUUGAUCAUCGGCAAGAUAAGUUAUUUACUAAAUAAUAGGAUUUAAUAACCUGGUGAGUUCGAAUCUCACAUUUUCCG
+>AF008220
+GGAGGAUUAGCUCAGCUGGGAGAGCAUCUGCCUUACAAGCAGAGGGUCGGCGGUUCGAGCCCGUCAUCCUCCA
+>Z11880
+GCCUUCCUAGCUCAGUGGUAGAGCGCACGGCUUUUAACCGUGUGGUCGUGGGUUCGAUCCCCACGGAAGGCG
+>X02172
+GCCUUUAUAGCUUAGUGGUAAAGCGAUAAACUGAAGAUUUAUUUACAUGUAGUUCGAUUCUCAUUAAGGGCA
+>M68929
+GCGGAUAUAACUUAGGGGUUAAAGUUGCAGAUUGUGGCUCUGAAAACACGGGUUCGAAUCCCGUUAUUCGCC