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Changeset 0:ebe28cac8d8b (2024-11-15)

Next changeset 1:2a156ec81e7a (2024-11-18)

Commit message:
planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671

added:
README.md
test-data/custom_trimmed_example.009.AA.html
test-data/custom_trimmed_example.009.AA.phy
test-data/example.004.AA.fasta
test-data/example.009.AA.fasta
test-data/trimmed_example.009.AA.html
test-data/trimmed_example.009.AA.mega
trimal.xml

diff -r 000000000000 -r ebe28cac8d8b README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Fri Nov 15 08:59:26 2024 +0000

[

@@ -0,0 +1,3 @@
+# trimAl
+
+[trimAl](https://github.com/inab/trimal), a tool for automated alignment trimming in large-scale phylogenetic analyses.

diff -r 000000000000 -r ebe28cac8d8b test-data/custom_trimmed_example.009.AA.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_trimmed_example.009.AA.html Fri Nov 15 08:59:26 2024 +0000

b'@@ -0,0 +1,74 @@\n+<!DOCTYPE html>\n+<html><head>\n+ <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" />\n+ <title>trimAl v1.5.0 Summary</title>\n+ <style type="text/css" media="all">\n+ #b { background-color: #3366ff; }\n+ #r { background-color: #cc0000; }\n+ #g { background-color: #33cc00; }\n+ #p { background-color: #ff6666; }\n+ #m { background-color: #cc33cc; }\n+ #o { background-color: #ff9900; }\n+ #c { background-color: #46C7C7; }\n+ #y { background-color: #FFFF00; }\n+ .sel { background-color: #B9B9B9; }\n+ .nsel { background-color: #E9E9E9; }\n+ .c1 { background-color: #FFFBF2; }\n+ .c2 { background-color: #FFF8CC; }\n+ .c3 { background-color: #FAF0BE; }\n+ .c4 { background-color: #F0EAD6; }\n+ .c5 { background-color: #F3E5AB; }\n+ .c6 { background-color: #F4C430; }\n+ .c7 { background-color: #C2B280; color: white; }\n+ .c8 { background-color: #DAA520; color: white; }\n+ .c9 { background-color: #B8860B; color: white; }\n+ .c10 { background-color: #918151; color: white; }\n+ .c11 { background-color: #967117; color: white; }\n+ .c12 { background-color: #6E5411; color: white; }\n+ </style>\n+ </head>\n+\n+ <body>\n+ <pre>\n+ Selected Sequences: 9 /Selected Residues: 63\n+ Deleted Sequences: 0 /Deleted Residues: 122\n+\n+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1= \n+ Similarity Scores: =0= <1e-6 <1e-5 <1e-4 <.001 <.010 <.100 <.250 <.500 <.750 <1.00 =1= \n+\n+ 10 20 30 40 50 60 70 80 90 100 110 120\n+ =========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+\n+ Csa004271 ---------------------------------MYMAMGHFFDRDDVALKNISEYFKECSEEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL\n+ Xtr21234 ----MISQVRQNYSHDCEA</spa'..b'span class=nsel> \n+\n+ Gaps Scores: \n+ Similarity Scores: \n+ </pre>\n+ </body>\n+</html>\n'

diff -r 000000000000 -r ebe28cac8d8b test-data/custom_trimmed_example.009.AA.phy
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/custom_trimmed_example.009.AA.phy Fri Nov 15 08:59:26 2024 +0000

@@ -0,0 +1,11 @@
+ 9 63
+Csa004271    --------------YMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Xtr21234     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+LcaH         SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Hsa167996    SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Mmu024661    SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Dre37936     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+LcaM         SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Tru14292     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+Ola20972     SQRQNDEAANNEAYYMFRDDALFSEEEAKNRGGPAALLVNLLLHDPDFELEQVKDNLELFDKH
+

diff -r 000000000000 -r ebe28cac8d8b test-data/example.004.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.004.AA.fasta Fri Nov 15 08:59:26 2024 +0000

@@ -0,0 +1,18 @@
+>Sp8
+FPWNGLQIHMMGIII
+
+>Sp17
+FPWNGLQIHMMGIII
+
+>Sp10
+FPWNGLQIHMMGIII
+
+>Sp26
+FPWNGLQIHMMGIII
+
+>Sp33
+FPWNGLQIHMMGIII
+
+>Sp6
+FPWNGLQIHMMGIII
+

diff -r 000000000000 -r ebe28cac8d8b test-data/example.009.AA.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.009.AA.fasta Fri Nov 15 08:59:26 2024 +0000

@@ -0,0 +1,45 @@
+>Csa004271
+---------------------------------MYMAMGHFFDRDDVALKNISEYFKECS
+EEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL
+HE--TANGDPEFQDFIEANFLHEQVDAIKKLKDYITNLKLVG---TGLGEFLFDKHFKSS
+-----
+>Xtr21234
+----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYFDRDDVALHHVAEFFKEQS
+KEERECAEKLMKCQNKRGGRIVLQDIKKPERDEWG--STLDAMQTALDLEKHVNQALLDL
+HNLATERKDPHICDFLESEHLDEQVKHMKKFGDHITNLKRLGVPQNGMGEYLFDKHSLS-
+-----
+>LcaH
+----MSSQVRQNFHQDCEAAINRQINLELYASYVYLSMAYYFDRDDQALHNFAKFFRHQS
+HEEREHAEKLMKLQNQRGGRIFLQDVRKPDRDEWG--SGVEALECALQLEKSVNQSLLDL
+HKLCSDHNDPHLCDFIETHYLDEQVKSIKELADWVTNLRRMGAPQNGMAEYLFDKHTLGK
+ES--S
+>Hsa167996
+MTTASTSQVRQNYHQDSEAAINRQINLELYASYVYLSMSYYFDRDDVALKNFAKYFLHQS
+HEEREHAEKLMKLQNQRGGRIFLQDIKKPDCDDWE--SGLNAMECALHLEKNVNQSLLEL
+HKLATDKNDPHLCDFIETHYLNEQVKAIKELGDHVTNLRKMGAPESGLAEYLFDKHTLGD
+SDNES
+>Mmu024661
+MTTASPSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQS
+HEEREHAEKLMKLQNQRGGRIFLQDIKKPDRDDWE--SGLNAMECALHLEKSVNQSLLEL
+HKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAGMAEYLFDKHTLGH
+GD-ES
+>Dre37936
+---METSQIRQNYVRDCEAAINKMINLELYAGYTYTSMAHYFKRDDVALPGFAKFFKKNS
+EEEREHAEKFMEFQNKRGGRIVLQDIKKPDRDVWG--NGLIAMQCALQLEKNVNQALLDL
+HKLATEMGDPHLCDFLETHYLNEQVEAIKKLGDHITNLSKMDAGNNRMAEYLFDKHTLDS
+-----
+>LcaM
+----MESQVRQNYHRDCEAAVNRMVNMEMFASYTYTSMAFYFSRDDVALPGFSHFFKENS
+DEEREHAEKLLSFQNKRGGHIFLQDIKKPERDEWG--SGLEAMQCALQLKKNVNQALLDL
+HKLASDHGDPHLCDFLETHYLNEQVEAIKKLGDYISNLSRMDAQKNKMAEYLFDKHSLGG
+KS---
+>Tru14292
+----MESQVRQNYHRDCEAAINKMINMELYASYTYTSMAFFFSRDDVALPGFAHFFKENS
+DEEREHAEKLLSFQNKRGGRIFLQDIKKPERDEWG--SGLEAMQCALQLEKKVNQALLDL
+HKLASDHVDPHLCDFLESHYLNEQVEAIKKLGDYITNLSRMDAQNNKMAEYLFDKHTLGS
+KS---
+>Ola20972
+----MESQVRQNYHRDCEAAINRMVNMELFASYTYTSMAFYFDRDDVALPGFSHFFKENS
+HEEKEHADKLLSFQNKRGGRIFLQDVKKPERDEWG--SGLEAMQCALQLEKNVNQALLDL
+HKVASDHKDPHMCDFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGS
+KS---
\ No newline at end of file

diff -r 000000000000 -r ebe28cac8d8b test-data/trimmed_example.009.AA.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmed_example.009.AA.html Fri Nov 15 08:59:26 2024 +0000

b'@@ -0,0 +1,71 @@\n+<!DOCTYPE html>\n+<html><head>\n+ <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1" />\n+ <title>trimAl v1.5.0 Summary</title>\n+ <style type="text/css" media="all">\n+ #b { background-color: #3366ff; }\n+ #r { background-color: #cc0000; }\n+ #g { background-color: #33cc00; }\n+ #p { background-color: #ff6666; }\n+ #m { background-color: #cc33cc; }\n+ #o { background-color: #ff9900; }\n+ #c { background-color: #46C7C7; }\n+ #y { background-color: #FFFF00; }\n+ .sel { background-color: #B9B9B9; }\n+ .nsel { background-color: #E9E9E9; }\n+ .c1 { background-color: #FFFBF2; }\n+ .c2 { background-color: #FFF8CC; }\n+ .c3 { background-color: #FAF0BE; }\n+ .c4 { background-color: #F0EAD6; }\n+ .c5 { background-color: #F3E5AB; }\n+ .c6 { background-color: #F4C430; }\n+ .c7 { background-color: #C2B280; color: white; }\n+ .c8 { background-color: #DAA520; color: white; }\n+ .c9 { background-color: #B8860B; color: white; }\n+ .c10 { background-color: #918151; color: white; }\n+ .c11 { background-color: #967117; color: white; }\n+ .c12 { background-color: #6E5411; color: white; }\n+ </style>\n+ </head>\n+\n+ <body>\n+ <pre>\n+ Selected Sequences: 9 /Selected Residues: 174\n+ Deleted Sequences: 0 /Deleted Residues: 11\n+\n+ Gaps Scores: =0= <.001 <.050 <.100 <.150 <.200 <.250 <.350 <.500 <.750 <1.00 =1= \n+\n+ 10 20 30 40 50 60 70 80 90 100 110 120\n+ =========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+=========+\n+ Csa004271 ---------------------------------MYMAMGHFFDRDDVALKNISEYFKECSEEEREHANKMIEFHNKRGGTTTYFPIKAPGSFDPANFNTIKAMNCALALEVNVNKSLLAL\n+ Xtr21234 ----MISQVRQNYSHDCEAAVNRMVNLEMYASYTYLSMSHYF<s'..b'd=m>DFLETHYLNEQVESIKKIGDHITNLTRMDAHTNKMAEYLFDKHTLGSKS---\n+\n+ Selected Cols: \n+\n+ Gaps Scores: \n+ </pre>\n+ </body>\n+</html>\n'

diff -r 000000000000 -r ebe28cac8d8b test-data/trimmed_example.009.AA.mega
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmed_example.009.AA.mega Fri Nov 15 08:59:26 2024 +0000

@@ -0,0 +1,58 @@
+#MEGA
+!Title ./test-data/example.009.AA.fasta;
+!Format DataType=protein NSeqs=9 Nsites=174 indel=- CodeTable=Standard;
+
+#Csa004271
+---------- ---------- ---------M YMAMGHFFDR DDVALKNISE
+YFKECSEEER EHANKMIEFH NKRGGTTTYF PIKAPGSFDP ANTIKAMNCA
+LALEVNVNKS LLALHE--TA NGDPEFQDFI EANFLHEQVD AIKKLKDYIT
+NLKLVG---T GLGEFLFDKH FKSS
+
+#Xtr21234
+MISQVRQNYS HDCEAAVNRM VNLEMYASYT YLSMSHYFDR DDVALHHVAE
+FFKEQSKEER ECAEKLMKCQ NKRGGRIVLQ DIKKPERDEW GSTLDAMQTA
+LDLEKHVNQA LLDLHNLATE RKDPHICDFL ESEHLDEQVK HMKKFGDHIT
+NLKRLGVPQN GMGEYLFDKH SLS-
+
+#LcaH
+MSSQVRQNFH QDCEAAINRQ INLELYASYV YLSMAYYFDR DDQALHNFAK
+FFRHQSHEER EHAEKLMKLQ NQRGGRIFLQ DVRKPDRDEW GSGVEALECA
+LQLEKSVNQS LLDLHKLCSD HNDPHLCDFI ETHYLDEQVK SIKELADWVT
+NLRRMGAPQN GMAEYLFDKH TLGK
+
+#Hsa167996
+STSQVRQNYH QDSEAAINRQ INLELYASYV YLSMSYYFDR DDVALKNFAK
+YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDCDDW ESGLNAMECA
+LHLEKNVNQS LLELHKLATD KNDPHLCDFI ETHYLNEQVK AIKELGDHVT
+NLRKMGAPES GLAEYLFDKH TLGD
+
+#Mmu024661
+SPSQVRQNYH QDAEAAINRQ INLELYASYV YLSMSCYFDR DDVALKNFAK
+YFLHQSHEER EHAEKLMKLQ NQRGGRIFLQ DIKKPDRDDW ESGLNAMECA
+LHLEKSVNQS LLELHKLATD KNDPHLCDFI ETYYLSEQVK SIKELGDHVT
+NLRKMGAPEA GMAEYLFDKH TLGH
+
+#Dre37936
+ETSQIRQNYV RDCEAAINKM INLELYAGYT YTSMAHYFKR DDVALPGFAK
+FFKKNSEEER EHAEKFMEFQ NKRGGRIVLQ DIKKPDRDVW GNGLIAMQCA
+LQLEKNVNQA LLDLHKLATE MGDPHLCDFL ETHYLNEQVE AIKKLGDHIT
+NLSKMDAGNN RMAEYLFDKH TLDS
+
+#LcaM
+MESQVRQNYH RDCEAAVNRM VNMEMFASYT YTSMAFYFSR DDVALPGFSH
+FFKENSDEER EHAEKLLSFQ NKRGGHIFLQ DIKKPERDEW GSGLEAMQCA
+LQLKKNVNQA LLDLHKLASD HGDPHLCDFL ETHYLNEQVE AIKKLGDYIS
+NLSRMDAQKN KMAEYLFDKH SLGG
+
+#Tru14292
+MESQVRQNYH RDCEAAINKM INMELYASYT YTSMAFFFSR DDVALPGFAH
+FFKENSDEER EHAEKLLSFQ NKRGGRIFLQ DIKKPERDEW GSGLEAMQCA
+LQLEKKVNQA LLDLHKLASD HVDPHLCDFL ESHYLNEQVE AIKKLGDYIT
+NLSRMDAQNN KMAEYLFDKH TLGS
+
+#Ola20972
+MESQVRQNYH RDCEAAINRM VNMELFASYT YTSMAFYFDR DDVALPGFSH
+FFKENSHEEK EHADKLLSFQ NKRGGRIFLQ DVKKPERDEW GSGLEAMQCA
+LQLEKNVNQA LLDLHKVASD HKDPHMCDFL ETHYLNEQVE SIKKIGDHIT
+NLTRMDAHTN KMAEYLFDKH TLGS
+

diff -r 000000000000 -r ebe28cac8d8b trimal.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/trimal.xml Fri Nov 15 08:59:26 2024 +0000

[

b'@@ -0,0 +1,131 @@\n+<tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">\n+ <description>for automated alignment trimming</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">1.5</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ </macros>\n+ <xrefs>\n+ <xref type="bio.tools">trimal</xref>\n+ </xrefs>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">trimal</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[ \n+ trimal -in \'$in\' -out \'$trimmed_output\' -htmlout \'$html_summary\' ${out_format_selector}\n+ #if $trimming_mode.mode_selector == "custom"\n+ -gapthreshold $trimming_mode.gapthreshold\n+ -simthreshold $trimming_mode.simthreshold\n+ -cons $trimming_mode.cons\n+ #else:\n+ $trimming_mode.mode_selector\n+ #end if\n+\n+ ]]></command>\n+ <inputs>\n+ <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" />\n+ <conditional name="trimming_mode">\n+ <param name="mode_selector" type="select" label="Select trimming mode from the list">\n+ <option value="-nogaps">nogaps - remove all positions with gaps in the alignment.</option>\n+ <option value="-noallgaps">noallgaps - remove columns composed only by gaps.</option>\n+ <option value="-gappyout">gappyout - only uses information based on gaps\' distribution.</option>\n+ <option value="-strict">strict - combine gappyout trimming with subsequent trimming based on an automatically selected similarity threshold. </option>\n+ <option value="-strictplus">strictplus - very similar to the strict method but the final step of the algorithm is slightly different. </option>\n+ <option value="-automated1">automated1 - heuristic approach to determine the optimal automatic method for trimming a given alignment. </option>\n+ <option value="custom">custom mode - eliminates a specified set of columns defined by the user.</option>\n+ </param>\n+ <when value="-nogaps" />\n+ <when value="-noallgaps"/>\n+ <when value="-gappyout"/>\n+ <when value="-strict"/>\n+ <when value="-strictplus"/>\n+ <when value="-automated1"/>\n+ <when value="custom">\n+ <param argument="-gapthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Gap threshold" help="1 - (fraction of sequences with a gap allowed)."/>\n+ <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Similarity threshold" help="Minimum average similarity allowed."/>\n+ <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="Minimum conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve."/>\n+ </when>\n+ </conditional>\n+ <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list">\n+ <option value="-clustal">CLUSTAL format</option>\n+ <option value="-fasta">FASTA format</option>\n+ <option value="-fasta_m10">FASTA format. Sequences name length up to 10 characters.</option>\n+ <option value="-nbrf">NBRF/PIR format</option>\n+ <option value="-nexus">NEXUS format</option>\n+ <option value="-mega">MEGA format</option>\n+ <option value="-phylip">PHYLIP/PHYLIP4 format</option>\n+ <option value="-phylip_m10">PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters</option>\n+ <option value="-phylip_paml">PHYLIP format compatible with PAML</option>\n+ <option value="-phylip_paml_m10">PHYLIP format'..b'el="Trimmed alignment.">\n+ <change_format>\n+ <when input="out_format_selector" value="-fasta" format="fasta" />\n+ <when input="out_format_selector" value="-fasta_m10" format="fasta" />\n+ <when input="out_format_selector" value="-phylip" format="phylip" />\n+ <when input="out_format_selector" value="-phylip_m10" format="phylip" />\n+ <when input="out_format_selector" value="-phylip_paml" format="phylip" />\n+ <when input="out_format_selector" value="-phylip_paml_m10" format="phylip" />\n+ <when input="out_format_selector" value="-phylip3.2" format="phylip" />\n+ <when input="out_format_selector" value="-phylip3.2_m10" format="phylip" />\n+ <when input="out_format_selector" value="-clustal" format="clustal" />\n+ <when input="out_format_selector" value="-mega" format="mega" />\n+ <when input="out_format_selector" value="-nbrf" format="pir" />\n+ <when input="out_format_selector" value="-nexus" format="nexus" />\n+ </change_format>\n+ </data>\n+ <data name="html_summary" format="html" label="trimal html summary."/>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="2">\n+ <param name="in" value="example.009.AA.fasta"/>\n+ <param name="mode_selector" value="-gappyout" />\n+ <param name="out_format_selector" value="-mega" />\n+ <output name="trimmed_output" file="trimmed_example.009.AA.mega" lines_diff="2"/>\n+ <output name="html_summary" file="trimmed_example.009.AA.html"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="in" value="example.009.AA.fasta"/>\n+ <param name="mode_selector" value="custom" />\n+ <param name="gapthreshold" value="0.5" />\n+ <param name="simthreshold" value="0.5" />\n+ <param name="cons" value="5" />\n+ <param name="out_format_selector" value="-phylip_paml_m10" />\n+ <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" ftype="phylip"/>\n+ <output name="html_summary" file="custom_trimmed_example.009.AA.html"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+TrimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.\n+\n+TrimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment.\n+These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided,\n+the consistency level of columns among alignments. Moreover, trimAl allows to manually select a set of columns and sequences to be removed from the alignment.\n+\n+TrimAl implements a series of automated algorithms that trim the alignment searching for optimum thresholds based on inherent characteristics\n+of the input alignment, to be used so that the signal-to-noise ratio after alignment trimming phase is increased. Learn more about the available trimming modes here: https://trimal.readthedocs.io/en/latest/algorithms.html\n+\n+Among trimAl\'s additional features, trimAl allows:\n+\n+- getting the complementary alignment (columns that were trimmed),\n+- to compute statistics from the alignment,\n+- to select the output file format, \n+- to get a summary of trimAl\'s trimming in HTML and SVG formats, \n+- and many other options.\n+\n+TrimAl webpage: https://trimal.readthedocs.io \n+\n+License\n+-------\n+This program is free software: you can redistribute it and/or modify \n+it under the terms of the GNU General Public License as published by \n+the Free Software Foundation, the last available version.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">doi:10.1093/bioinformatics/btp348</citation>\n+ </citations>\n+</tool>\n\\ No newline at end of file\n'