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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
author iuc
date Tue, 02 Dec 2025 09:27:37 +0000
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5acf23babd9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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1 <tool id="amas_concat" name="AMAS concat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>concatenate multiple alignments</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <xrefs>
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9 <xref type="bio.tools">amas</xref>
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10 </xrefs>
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12 <expand macro="requirements" />
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13 <expand macro="version_command" />
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15 <command detect_errors="exit_code"><![CDATA[
5acf23babd9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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16 #import re
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17 set -eu;
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19 @SNIFF_INPUT_FORMAT@
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21 @CHECK_INTERLEAVED@
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23 @SYMLINK_INPUTS@
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25 python -m amas.AMAS
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26 concat
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27 --concat-part partitions.txt
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28 --concat-out concatenated.out
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29 --part-format $part_format
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30 --out-format $out_format
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31 --in-files
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32 @INPUT_FILENAMES@
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33 --in-format "\${IN_FORMAT}"
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34 --data-type $data_type
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35 --cores "\${GALAXY_SLOTS:-1}"
5acf23babd9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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36 $check_align
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37 ]]></command>
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38
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39 <inputs>
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40 <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequences to concatenate" multiple="true"
5acf23babd9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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41 help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." />
5acf23babd9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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42 <expand macro="output_format" label="Select output format for concatenated alignment" />
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43 <param name="part_format" type="select" label="Format of the partitions file"
5acf23babd9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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44 help="A file defining how the concatenated alignment is split into separate gene/locus regions. Each line specifies a partition name and its position range (e.g., 'gene1 = 1-500' or 'DNA, gene1 = 1-500' for RAxML format).">
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45 <option value="unspecified" selected="true">unspecified</option>
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46 <option value="nexus">nexus</option>
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47 <option value="raxml">raxml</option>
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48 </param>
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49 <expand macro="data_type" />
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50 <expand macro="check_align" />
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51 </inputs>
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52
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53 <outputs>
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54 <data name="output" from_work_dir="concatenated.out" format="txt" label="${tool.name} on ${on_string}: Concatenated alignment">
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55 <change_format>
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56 <when input="out_format" value="fasta" format="fasta" />
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57 <when input="out_format" value="phylip" format="phylip" />
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58 <when input="out_format" value="phylip-int" format="phylip" />
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59 <when input="out_format" value="nexus" format="nex" />
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60 <when input="out_format" value="nexus-int" format="nex" />
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61 </change_format>
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62 </data>
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63 <data name="partitions_out" from_work_dir="partitions.txt" format="txt" label="${tool.name} on ${on_string}: Partition file">
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64 <change_format>
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65 <!-- Untitled and RAxML partition formats have no current equivalent datatypes so are outputted as txt by default -->
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66 <when input="part_format" value="nexus" format="nex" />
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67 </change_format>
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68 </data>
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69 </outputs>
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70
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71 <tests>
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72 <test expect_num_outputs="2">
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73 <param name="input_files" value="inputs/concat_1.fasta,inputs/concat_2.fasta" />
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74 <param name="out_format" value="phylip" />
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75 <param name="part_format" value="nexus" />
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76 <param name="data_type" value="dna" />
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77 <param name="check_align" value="false" />
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78 <output name="output" file="outputs/expected_concat.phylip" ftype="phylip" />
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79 <output name="partitions_out" file="outputs/expected_partitions.nex" ftype="nex" />
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80 </test>
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81 <test expect_num_outputs="2">
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82 <param name="input_files" value="inputs/concat_1.fasta,inputs/concat_2.fasta" />
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83 <param name="out_format" value="fasta" />
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84 <param name="part_format" value="raxml" />
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85 <param name="data_type" value="dna" />
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86 <param name="check_align" value="false" />
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87 <output name="output" file="outputs/expected_concat_fasta.fas" ftype="fasta" />
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88 <output name="partitions_out" file="outputs/expected_partitions_raxml.txt" ftype="txt" />
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89 </test>
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90 <!-- Interleave tests: amas starts interleaving when sequences have lines > 500 characters -->
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91 <test expect_num_outputs="2">
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92 <param name="input_files" value="inputs/concat_int_1.phylip,inputs/concat_int_2.phylip" />
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93 <param name="out_format" value="nexus-int" />
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94 <param name="part_format" value="unspecified" />
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95 <param name="data_type" value="dna" />
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96 <param name="check_align" value="false" />
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97 <output name="output" file="outputs/expected_concat_int.nex" ftype="nex" />
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98 <output name="partitions_out" file="outputs/expected_partitions_int.txt" ftype="txt" />
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99 </test>
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100 <!-- Nexus interleave tests for: 'INTERLEAVE', 'Interleave=yes;', no interleave flag -->
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101 <test expect_num_outputs="2">
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102 <param name="input_files" value="inputs/concat_int_1.nex,inputs/concat_int_2.nex,inputs/concat_int_3.nex" />
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103 <param name="out_format" value="nexus-int" />
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104 <param name="part_format" value="unspecified" />
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105 <param name="data_type" value="dna" />
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106 <param name="check_align" value="false" />
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107 <output name="output" file="outputs/expected_concat_int_multi.nex" ftype="nex" />
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108 <output name="partitions_out" file="outputs/expected_partitions_int_multi.txt" ftype="txt" />
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109 </test>
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110 </tests>
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111
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112 <help><![CDATA[
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113 **What it does**
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114
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115 AMAS Concat combines multiple sequence alignments into a single concatenated alignment, commonly used in phylogenomic analyses.
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116
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117 **Inputs**
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118
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119 - **Multiple alignment files**: Select 2 or more pre-aligned sequence files (FASTA, PHYLIP, or NEXUS format)
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120 - **Input format**: Specify the format of your input files
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121 - **Partition format**: Specify how you want the partition file to be formatted (Unspecified, RAxML, NEXUS)
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122 - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences
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123 - **Output format**: Select the desired format for the concatenated alignment
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124
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125 **Outputs**
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126
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127 1. **Concatenated alignment**: A single file containing all input alignments joined end-to-end
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128 2. **Partitions file**: Defines the boundaries of each original alignment within the concatenated file
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129
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130 @PARTITIONS_HELP@
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131
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132 **Use cases**
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133
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134 - **Multi-locus phylogenomics**: Combine hundreds of genes for species tree inference
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135 - **Partitioned phylogenetic analysis**: Apply different evolutionary models to different genes using tools like RAxML or IQ-TREE
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136 - **Supermatrix construction**: Create dataset for concatenation-based phylogenetic methods
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137 - **Increased phylogenetic signal**: Leverage information from multiple loci to resolve difficult nodes
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138 - **Comparative analyses**: Prepare datasets for testing hypotheses across multiple genomic regions
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139
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140 @AMAS_SHARED_HELP@
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141 ]]></help>
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142
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143 <expand macro="citations" />
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144 </tool>