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[tool update] Trimal #6577

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6 changes: 4 additions & 2 deletions tools/trimal/.shed.yml
Original file line number Diff line number Diff line change
@@ -1,9 +1,11 @@
categories:
- Sequence Analysis
- Phylogenetics
description: Tool for automated alignment trimming
homepage_url: https://trimal.readthedocs.io
long_description: trimAl is a tool for the automated removal of spurious sequences
or poorly aligned regions from a multiple sequence alignment.
homepage_url: https://trimal.readthedocs.io
name: trimal
owner: iuc
remote_repository_url: https://github.com/inab/trimal
remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal
type: unrestricted
37 changes: 37 additions & 0 deletions tools/trimal/test-data/custom_trimmed_example.009.AA.nexus
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
#NEXUS
BEGIN DATA;
DIMENSIONS NTAX=9 NCHAR=63;
FORMAT DATATYPE=PROTEIN INTERLEAVE=yes GAP=-;
[Name: Csa004271 Len: 63]
[Name: Xtr21234 Len: 63]
[Name: LcaH Len: 63]
[Name: Hsa167996 Len: 63]
[Name: Mmu024661 Len: 63]
[Name: Dre37936 Len: 63]
[Name: LcaM Len: 63]
[Name: Tru14292 Len: 63]
[Name: Ola20972 Len: 63]

MATRIX
Csa004271 ---------- ----YMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
Xtr21234 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
LcaH SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
Hsa167996 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
Mmu024661 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
Dre37936 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
LcaM SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
Tru14292 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL
Ola20972 SQRQNDEAAN NEAYYMFRDD ALFSEEEAKN RGGPAALLVN LLLHDPDFEL

Csa004271 EQVKDNLELF DKH
Xtr21234 EQVKDNLELF DKH
LcaH EQVKDNLELF DKH
Hsa167996 EQVKDNLELF DKH
Mmu024661 EQVKDNLELF DKH
Dre37936 EQVKDNLELF DKH
LcaM EQVKDNLELF DKH
Tru14292 EQVKDNLELF DKH
Ola20972 EQVKDNLELF DKH

;
END;
12 changes: 12 additions & 0 deletions tools/trimal/test-data/custom_trimmed_window_example.005.AA.fasta
Original file line number Diff line number Diff line change
@@ -0,0 +1,12 @@
>Sp8
FPWNGLQIHMMGIII---------------------------------------------
>Sp17
FPWNGLQIHMMGIIIIIIIIIIIIIIIIII------------------------------
>Sp10
FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------
>Sp26
FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
>Sp33
FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
>Sp6
FPWNGLQIHMMGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
54 changes: 54 additions & 0 deletions tools/trimal/test-data/custom_trimmed_window_example.009.AA.html
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@@ -0,0 +1,54 @@
<!DOCTYPE html>
<html><head>
<meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" />
<title>trimAl v1.5.0 Summary</title>
<style type="text/css" media="all">
#b { background-color: #3366ff; }
#r { background-color: #cc0000; }
#g { background-color: #33cc00; }
#p { background-color: #ff6666; }
#m { background-color: #cc33cc; }
#o { background-color: #ff9900; }
#c { background-color: #46C7C7; }
#y { background-color: #FFFF00; }
.sel { background-color: #B9B9B9; }
.nsel { background-color: #E9E9E9; }
.c1 { background-color: #FFFBF2; }
.c2 { background-color: #FFF8CC; }
.c3 { background-color: #FAF0BE; }
.c4 { background-color: #F0EAD6; }
.c5 { background-color: #F3E5AB; }
.c6 { background-color: #F4C430; }
.c7 { background-color: #C2B280; color: white; }
.c8 { background-color: #DAA520; color: white; }
.c9 { background-color: #B8860B; color: white; }
.c10 { background-color: #918151; color: white; }
.c11 { background-color: #967117; color: white; }
.c12 { background-color: #6E5411; color: white; }
</style>
</head>

<body>
<pre>
<span class=sel>Selected Sequences: 6 /Selected Residues: 60</span>
<span class=nsel>Deleted Sequences: 0 /Deleted Residues: 30</span>

Gaps Scores: <span class=c1> =0= </span><span class=c2> <.001 </span><span class=c3> <.050 </span><span class=c4> <.100 </span><span class=c5> <.150 </span><span class=c6> <.200 </span><span class=c7> <.250 </span><span class=c8> <.350 </span><span class=c9> <.500 </span><span class=c10> <.750 </span><span class=c11> <1.00 </span><span class=c12> =1= </span>
Similarity Scores: <span class=c1> =0= </span><span class=c2> <1e-6 </span><span class=c3> <1e-5 </span><span class=c4> <1e-4 </span><span class=c5> <.001 </span><span class=c6> <.010 </span><span class=c7> <.100 </span><span class=c8> <.250 </span><span class=c9> <.500 </span><span class=c10> <.750 </span><span class=c11> <1.00 </span><span class=c12> =1= </span>

10 20 30 40 50 60 70 80 90
=========+=========+=========+=========+=========+=========+=========+=========+=========+
<span class=sel>Sp8</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>---------------------------------------------------------------------------
<span class=sel>Sp17</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>------------------------------------------------------------
<span class=sel>Sp10</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>---------------------------------------------
<span class=sel>Sp26</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIII------------------------------
<span class=sel>Sp33</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIIIIIIIIIIIIIIIIII---------------
<span class=sel>Sp6</span> <span id=b>F</span><span id=y>P</span><span id=b>W</span><span id=g>N</span><span id=o>G</span><span id=b>L</span><span id=g>Q</span><span id=b>I</span><span id=c>H</span><span id=b>M</span><span id=b>M</span><span id=o>G</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span><span id=b>I</span>IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

Selected Cols: <span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=sel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span><span class=nsel> </span>

Gaps Scores: <span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c11> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c10> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c8> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span><span class=c6> </span>
Similarity Scores: <span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c12> </span><span class=c11> </span><span class=c11> </span><span class=c10> </span><span class=c10> </span><span class=c9> </span><span class=c9> </span><span class=c8> </span><span class=c8> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span><span class=c1> </span>
</pre>
</body>
</html>
9 changes: 9 additions & 0 deletions tools/trimal/test-data/example.002.AA.out.phy
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
6 19
Sp17 LIGFLLLWQGLDLNKMPVF
Sp10 V--IMLAWLGLEINMMVII
Sp8 Y-GIVLPWNGLQIHMMGII
Sp33 A-GLHMAWGGLEINKQAIL
Sp6 L-GIYLAWLGLEINMMAII
Sp26 L-GLFLAWLGLEINMMAQI


8 changes: 8 additions & 0 deletions tools/trimal/test-data/example.002.AA.phy
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
6 60
Sp17 --------FAYTAPD---LLLIGFLLKTVA-T-FG--DTWF-----QLWQGLDLNKMPVF
Sp10 ----------DPAVL----FV--IMLGTIT-K-FS--SEWF-----FAWLGLEINMMVII
Sp8 ----------GLGKV---IVY-GIVLGTKS-DQFSNWVVWL-----FPWNGLQIHMMGII
Sp33 -----------PTIL---NIA-GLHMETDI-N-FS--LAWF-----QAWGGLEINKQAIL
Sp6 ----------ASGAI---LTL-GIYLFTLC-AVIS--VSWY-----LAWLGLEINMMAII
Sp26 AAAAAAAA----ALL---TYL-GLFLGTDY-----EN---FAAAAANAWLGLEINMMAQI

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