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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal commit 810dbb9e462f48ddc9e817a149b8c5b796221ea4
author iuc
date Wed, 03 Dec 2025 15:44:18 +0000
parents 46bca620b895
children
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3
1316b4fa3c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal commit 810dbb9e462f48ddc9e817a149b8c5b796221ea4
iuc
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1 <tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
0
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2 <description>for automated alignment trimming</description>
b0891bedcb5b planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671
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3 <macros>
3
1316b4fa3c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal commit 810dbb9e462f48ddc9e817a149b8c5b796221ea4
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4 <token name="@TOOL_VERSION@">1.5.1</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
1316b4fa3c4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal commit 810dbb9e462f48ddc9e817a149b8c5b796221ea4
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6 <token name="@PROFILE@">23.0</token>
0
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7 </macros>
2
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8 <edam_topics>
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9 <edam_topic>topic_3293</edam_topic> <!-- phylogenetics -->
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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10 <edam_topic>topic_0080</edam_topic> <!-- sequence analysis -->
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11 </edam_topics>
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12 <edam_operations>
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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13 <edam_operation>operation_3192</edam_operation> <!--sequence trimming -->
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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14 </edam_operations>
0
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15 <xrefs>
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16 <xref type="bio.tools">trimal</xref>
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17 </xrefs>
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18 <requirements>
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19 <requirement type="package" version="@TOOL_VERSION@">trimal</requirement>
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20 </requirements>
2
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21 <command detect_errors="aggressive"><![CDATA[
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22
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23 trimal -in '$in'
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24 -out '$trimmed_output'
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25 ${out_format_selector}
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26
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27 #unless $trimming_mode.mode_selector == "manual"
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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28 -htmlout '$html_summary'
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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29 #end unless
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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30
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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31 #if $trimming_mode.mode_selector == "custom"
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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32 -gapthreshold $trimming_mode.gapthreshold
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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33 -simthreshold $trimming_mode.simthreshold
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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34 -cons $trimming_mode.cons
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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35
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36 #if $trimming_mode.w
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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37 -w $trimming_mode.w
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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38 #else
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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39 #if $trimming_mode.gw
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40 -gw $trimming_mode.gw
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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41 #end if
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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42 #if $trimming_mode.sw
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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43 -sw $trimming_mode.sw
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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44 #end if
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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45 #if $trimming_mode.cw
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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46 -cw $trimming_mode.cw
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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47 #end if
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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48 #end if
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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49 #else if $trimming_mode.mode_selector == "manual"
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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50 #if $trimming_mode.selectcols
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51 -selectcols { $trimming_mode.selectcols }
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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52 #end if
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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53 #if $trimming_mode.selectseqs
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54 -selectseqs { $trimming_mode.selectseqs }
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55 #end if
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56 #else
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57 $trimming_mode.mode_selector
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58 #end if
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59
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60 #if $resoverlap
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61 -resoverlap $resoverlap
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62 #end if
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63 #if $seqoverlap
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64 -seqoverlap $seqoverlap
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65 #end if
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66
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67 #if $statistics
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68 -sgc
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69 -sgt
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70 -ssc
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71 -sst
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72 -sident
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73 -soverlap
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74 | tee '$statsout'
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75 #end if
0
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76 ]]></command>
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77 <inputs>
3
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78 <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega,txt" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)"/>
0
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79 <conditional name="trimming_mode">
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80 <param name="mode_selector" type="select" label="Select trimming mode from the list">
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81 <option value="-nogaps">nogaps - remove all positions with gaps in the alignment.</option>
b0891bedcb5b planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671
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82 <option value="-noallgaps">noallgaps - remove columns composed only by gaps.</option>
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83 <option value="-gappyout">gappyout - only uses information based on gaps' distribution.</option>
b0891bedcb5b planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671
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84 <option value="-strict">strict - combine gappyout trimming with subsequent trimming based on an automatically selected similarity threshold. </option>
b0891bedcb5b planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671
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85 <option value="-strictplus">strictplus - very similar to the strict method but the final step of the algorithm is slightly different. </option>
b0891bedcb5b planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671
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86 <option value="-automated1">automated1 - heuristic approach to determine the optimal automatic method for trimming a given alignment. </option>
2
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87 <option value="custom">custom mode - define trimming parameters yourself.</option>
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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88 <option value="manual">manual mode - specify columns or sequences to remove</option>
0
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89 </param>
3
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90 <when value="-nogaps"/>
0
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91 <when value="-noallgaps"/>
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92 <when value="-gappyout"/>
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93 <when value="-strict"/>
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94 <when value="-strictplus"/>
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95 <when value="-automated1"/>
2
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96 <when value="manual">
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97 <param argument="-selectcols" type="text" optional="true" label="Columns to be removed from alignment" help="Example: '2,4,8-12'; Range: [0 - (Number of Columns - 1)]">
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98 <validator type="regex" message="must be comma-separated list of whole numbers">(\d+)([,-]\d+)*</validator>
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99 </param>
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100 <param argument="-selectseqs" type="text" optional="true" label="Sequences to be removed from alignment" help="Example: '2,4,8-12'; Range: [0 - (Number of Sequences - 1)]">
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101 <validator type="regex" message="must be comma-separated list of whole numbers">(\d+)([,-]\d+)*</validator>
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102 </param>
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103 </when>
0
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104 <when value="custom">
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105 <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)."/>
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106 <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Similarity threshold" help="Minimum average similarity allowed."/>
2
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107 <param argument="-conthreshold" type="float" optional="true" min="0" max="100" label="Consistency Threshold. Minimum consistency value required" help="Range: [0 - 1]. Not allowed in combination with inputfile."/>
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108 <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."/>
2
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109 <param argument="-clusters" type="integer" optional="true" min="0" label="Clusters. Get the most Nth representatives sequences from a given alignment." help="Range: [1 - (Number of sequences)]"/>
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110 <param argument="-maxidentity" type="float" optional="true" min="0" max="1" label="Max Identity. Get the representatives sequences for a given identity threshold. " help="Range: [0 - 1]"/>
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111 <param argument="-w" type="integer" optional="true" min="0" label="Window frame size - general" help="score of position i is the average of the window (i - n) to (i + n). Will override specific sizes set below"/>
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112 <param argument="-gw" type="integer" optional="true" min="0" label="Window frame size applied to Gaps" help="score of position i is the average of the window (i - n) to (i + n)."/>
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113 <param argument="-sw" type="integer" optional="true" min="0" label="Window frame size applied to Similarity" help="score of position i is the average of the window (i - n) to (i + n)."/>
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114 <param argument="-cw" type="integer" optional="true" min="0" label="Window frame size applied to Consistency" help="score of position i is the average of the window (i - n) to (i + n)."/>
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115 </when>
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116 </conditional>
2
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117 <param argument="-resoverlap" type="float" optional="true" min="0" max="1" label="Residue overlap" help="Minimum overlap of a positions with other positions in the column to be considered a “good position”. Range: [0-1]. Must be used in combination with Sequence overlap."/>
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118 <param argument="-seqoverlap" type="integer" optional="true" min="0" max="100" label="Sequence overlap" help="Minimum percentage of “good positions” that a sequence must have in order to be conserved. Range: [0-100]. Must be used in combination with Residue overlap."/>
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119
0
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120 <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list">
2
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121 <option value="" selected="true">Same as input (default)</option>
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122 <option value="-clustal">CLUSTAL format</option>
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123 <option value="-fasta">FASTA format</option>
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124 <option value="-fasta_m10">FASTA format. Sequences name length up to 10 characters.</option>
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125 <option value="-nbrf">NBRF/PIR format</option>
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126 <option value="-nexus">NEXUS format</option>
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127 <option value="-mega">MEGA format</option>
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128 <option value="-phylip">PHYLIP/PHYLIP4 format</option>
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129 <option value="-phylip_m10">PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters</option>
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130 <option value="-phylip_paml">PHYLIP format compatible with PAML</option>
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131 <option value="-phylip_paml_m10">PHYLIP format compatible with PAML. Sequences name length up to 10 characters.</option>
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132 <option value="-phylip3.2">PHYLIP3.2 format</option>
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133 <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option>
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134 </param>
2
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135 <param name="statistics" type="boolean" checked="false" label="Output trimming statistics?"/>
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136 </inputs>
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137 <outputs>
3
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138 <data name="trimmed_output" format_source="in" label="${tool.name} on ${on_string}: Trimmed alignment">
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139 <change_format>
3
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140 <when input="out_format_selector" value="-fasta" format="fasta"/>
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141 <when input="out_format_selector" value="-fasta_m10" format="fasta"/>
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142 <when input="out_format_selector" value="-phylip" format="phylip"/>
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143 <when input="out_format_selector" value="-phylip_m10" format="phylip"/>
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144 <when input="out_format_selector" value="-phylip_paml" format="phylip"/>
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145 <when input="out_format_selector" value="-phylip_paml_m10" format="phylip"/>
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146 <when input="out_format_selector" value="-phylip3.2" format="phylip"/>
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147 <when input="out_format_selector" value="-phylip3.2_m10" format="phylip"/>
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148 <when input="out_format_selector" value="-clustal" format="clustal"/>
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149 <when input="out_format_selector" value="-mega" format="mega"/>
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150 <when input="out_format_selector" value="-nbrf" format="pir"/>
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151 <when input="out_format_selector" value="-nexus" format="nexus"/>
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152 </change_format>
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153 </data>
2
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154 <data name="html_summary" format="html" label="${tool.name} on ${on_string}: HTML report">
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155 <filter> trimming_mode['mode_selector'] != 'manual' </filter>
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156 </data>
3
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157 <data name="statsout" format="txt" label="${tool.name} on ${on_string}: Statistics">
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158 <filter> statistics </filter>
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159 </data>
0
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160 </outputs>
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161 <tests>
3
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162 <!-- Test 01: automated trim setting -->
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163 <test expect_num_outputs="2">
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164 <param name="in" value="example.009.AA.fasta"/>
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165 <conditional name="trimming_mode">
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166 <param name="mode_selector" value="-gappyout"/>
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167 </conditional>
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168 <param name="out_format_selector" value="-mega"/>
2
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169 <output name="trimmed_output" file="trimmed_example.009.AA.mega" ftype="mega" lines_diff="2"/>
3
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170 <output name="html_summary" file="trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
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171 </test>
3
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172 <!-- Test 02: custom trim setting -->
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173 <test expect_num_outputs="2">
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174 <param name="in" value="example.009.AA.fasta"/>
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175 <conditional name="trimming_mode">
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176 <param name="mode_selector" value="custom"/>
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177 <param name="gapthreshold" value="0.5"/>
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178 <param name="simthreshold" value="0.5"/>
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179 <param name="cons" value="5"/>
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180 </conditional>
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181 <param name="out_format_selector" value="-phylip_paml_m10"/>
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182 <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" ftype="phylip"/>
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183 <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
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184 </test>
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185 <!-- Test 03: additional custom trim setting -->
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186 <test expect_num_outputs="2">
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187 <param name="in" value="example.009.AA.fasta"/>
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188 <conditional name="trimming_mode">
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189 <param name="mode_selector" value="custom"/>
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190 <param name="gapthreshold" value="0.75"/>
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191 <param name="simthreshold" value="0.8"/>
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192 <param name="cons" value="5"/>
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193 <param name="conthreshold" value="0.5"/>
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194 <param name="clusters" value="4"/>
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195 <param name="maxidentity" value="0.8"/>
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196 </conditional>
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197 <param name="out_format_selector" value="-nexus"/>
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198 <output name="trimmed_output" file="custom_trimmed_example.009.AA.nexus" ftype="nexus"/>
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199 <output name="html_summary" file="custom_trimmed_example.009.AA.html" ftype="html" lines_diff="4"/>
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200 </test>
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201 <!-- Test 04: Window settings -->
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202 <test expect_num_outputs="2">
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203 <param name="in" value="example.005.AA.fasta"/>
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204 <conditional name="trimming_mode">
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205 <param name="mode_selector" value="custom"/>
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206 <param name="gapthreshold" value="0.5"/>
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207 <param name="simthreshold" value="0.5"/>
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208 <param name="conthreshold" value="0.5"/>
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209 <param name="gw" value="3"/>
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210 <param name="sw" value="4"/>
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211 <param name="cw" value="5"/>
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212 </conditional>
2
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213 <output name="trimmed_output" file="custom_trimmed_window_example.005.AA.fasta" ftype="fasta"/>
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214 <output name="html_summary" file="custom_trimmed_window_example.009.AA.html" ftype="html" lines_diff="4"/>
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215 </test>
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216 <!-- Test 05: with phylip input and output statistics -->
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217 <test expect_num_outputs="3">
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218 <param name="in" value="example.002.AA.phy" ftype="phylip"/>
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219 <conditional name="trimming_mode">
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220 <param name="mode_selector" value="-strict"/>
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221 </conditional>
2
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222 <param name="statistics" value="true"/>
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223 <output name="trimmed_output" file="example.002.AA.out.phy" ftype="phylip"/>
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224 <output name="html_summary" file="example.002.AA.report.html" ftype="html" lines_diff="4"/>
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225 <output name="statsout" file="example.002.AA.stats.txt" ftype="txt"/>
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226 </test>
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227 <!-- Test 06: with overlap trimming -->
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228 <test expect_num_outputs="2">
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229 <param name="in" value="example.005.AA.fasta" ftype="fasta"/>
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230 <conditional name="trimming_mode">
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231 <param name="mode_selector" value="-nogaps"/>
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232 </conditional>
2
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233 <param name="resoverlap" value="0.8"/>
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234 <param name="seqoverlap" value="6"/>
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235 <output name="trimmed_output" file="example.005.AA.out.overlaptrim.fasta" ftype="fasta"/>
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236 <output name="html_summary" file="example.005.AA.report.overlaptrim.html" ftype="html" lines_diff="4"/>
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237 </test>
3
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238 <!-- Test 07: with manual trimming -->
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239 <test expect_num_outputs="1">
2
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240 <param name="in" value="example.009.AA.fasta" ftype="fasta"/>
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241 <conditional name="trimming_mode">
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242 <param name="mode_selector" value="manual"/>
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243 <param name="selectcols" value="2,4,7-9"/>
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244 <param name="selectseqs" value="1,3,5-7"/>
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245 </conditional>
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246 <output name="trimmed_output" file="example.009.AA.out.notrim.fasta" ftype="fasta"/>
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247 </test>
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248 </tests>
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249 <help><![CDATA[
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250
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251 TrimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.
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252
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253 TrimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment.
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254 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,
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255 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.
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256
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257 TrimAl implements a series of automated algorithms that trim the alignment searching for optimum thresholds based on inherent characteristics
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258 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
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259
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260 Among trimAl's additional features, trimAl allows:
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261
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262 - getting the complementary alignment (columns that were trimmed),
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263 - to compute statistics from the alignment,
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264 - to select the output file format,
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265 - to get a summary of trimAl's trimming in HTML and SVG formats,
0
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266 - and many other options.
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267
2
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268 TrimAl webpage: https://trimal.readthedocs.io
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269
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270 License
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271 -------
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46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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272 This program is free software: you can redistribute it and/or modify
46bca620b895 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trimal commit f6575973c143041bfbcb8afa12077c77e65e91a5
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273 it under the terms of the GNU General Public License as published by
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274 the Free Software Foundation, the last available version.
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275 ]]></help>
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276 <citations>
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277 <citation type="doi">10.1093/bioinformatics/btp348</citation>
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278 </citations>
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279 </tool>