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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 09:26:01 +0000
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1 <tool id="amas_concat" name="AMAS concat" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>concatenate multiple alignments</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <xrefs>
9 <xref type="bio.tools">amas</xref>
10 </xrefs>
11
12 <expand macro="requirements" />
13 <expand macro="version_command" />
14
15 <command detect_errors="exit_code"><![CDATA[
16 #import re
17 set -eu;
18
19 @SNIFF_INPUT_FORMAT@
20
21 @CHECK_INTERLEAVED@
22
23 @SYMLINK_INPUTS@
24
25 python -m amas.AMAS
26 concat
27 --concat-part partitions.txt
28 --concat-out concatenated.out
29 --part-format $part_format
30 --out-format $out_format
31 --in-files
32 @INPUT_FILENAMES@
33 --in-format "\${IN_FORMAT}"
34 --data-type $data_type
35 --cores "\${GALAXY_SLOTS:-1}"
36 $check_align
37 ]]></command>
38
39 <inputs>
40 <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequences to concatenate" multiple="true"
41 help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." />
42 <expand macro="output_format" label="Select output format for concatenated alignment" />
43 <param name="part_format" type="select" label="Format of the partitions file"
44 help="A file defining how the concatenated alignment is split into separate gene/locus regions. Each line specifies a partition name and its position range (e.g., 'gene1 = 1-500' or 'DNA, gene1 = 1-500' for RAxML format).">
45 <option value="unspecified" selected="true">unspecified</option>
46 <option value="nexus">nexus</option>
47 <option value="raxml">raxml</option>
48 </param>
49 <expand macro="data_type" />
50 <expand macro="check_align" />
51 </inputs>
52
53 <outputs>
54 <data name="output" from_work_dir="concatenated.out" format="txt" label="${tool.name} on ${on_string}: Concatenated alignment">
55 <change_format>
56 <when input="out_format" value="fasta" format="fasta" />
57 <when input="out_format" value="phylip" format="phylip" />
58 <when input="out_format" value="phylip-int" format="phylip" />
59 <when input="out_format" value="nexus" format="nex" />
60 <when input="out_format" value="nexus-int" format="nex" />
61 </change_format>
62 </data>
63 <data name="partitions_out" from_work_dir="partitions.txt" format="txt" label="${tool.name} on ${on_string}: Partition file">
64 <change_format>
65 <!-- Untitled and RAxML partition formats have no current equivalent datatypes so are outputted as txt by default -->
66 <when input="part_format" value="nexus" format="nex" />
67 </change_format>
68 </data>
69 </outputs>
70
71 <tests>
72 <test expect_num_outputs="2">
73 <param name="input_files" value="inputs/concat_1.fasta,inputs/concat_2.fasta" />
74 <param name="out_format" value="phylip" />
75 <param name="part_format" value="nexus" />
76 <param name="data_type" value="dna" />
77 <param name="check_align" value="false" />
78 <output name="output" file="outputs/expected_concat.phylip" ftype="phylip" />
79 <output name="partitions_out" file="outputs/expected_partitions.nex" ftype="nex" />
80 </test>
81 <test expect_num_outputs="2">
82 <param name="input_files" value="inputs/concat_1.fasta,inputs/concat_2.fasta" />
83 <param name="out_format" value="fasta" />
84 <param name="part_format" value="raxml" />
85 <param name="data_type" value="dna" />
86 <param name="check_align" value="false" />
87 <output name="output" file="outputs/expected_concat_fasta.fas" ftype="fasta" />
88 <output name="partitions_out" file="outputs/expected_partitions_raxml.txt" ftype="txt" />
89 </test>
90 <!-- Interleave tests: amas starts interleaving when sequences have lines > 500 characters -->
91 <test expect_num_outputs="2">
92 <param name="input_files" value="inputs/concat_int_1.phylip,inputs/concat_int_2.phylip" />
93 <param name="out_format" value="nexus-int" />
94 <param name="part_format" value="unspecified" />
95 <param name="data_type" value="dna" />
96 <param name="check_align" value="false" />
97 <output name="output" file="outputs/expected_concat_int.nex" ftype="nex" />
98 <output name="partitions_out" file="outputs/expected_partitions_int.txt" ftype="txt" />
99 </test>
100 <!-- Nexus interleave tests for: 'INTERLEAVE', 'Interleave=yes;', no interleave flag -->
101 <test expect_num_outputs="2">
102 <param name="input_files" value="inputs/concat_int_1.nex,inputs/concat_int_2.nex,inputs/concat_int_3.nex" />
103 <param name="out_format" value="nexus-int" />
104 <param name="part_format" value="unspecified" />
105 <param name="data_type" value="dna" />
106 <param name="check_align" value="false" />
107 <output name="output" file="outputs/expected_concat_int_multi.nex" ftype="nex" />
108 <output name="partitions_out" file="outputs/expected_partitions_int_multi.txt" ftype="txt" />
109 </test>
110 </tests>
111
112 <help><![CDATA[
113 **What it does**
114
115 AMAS Concat combines multiple sequence alignments into a single concatenated alignment, commonly used in phylogenomic analyses.
116
117 **Inputs**
118
119 - **Multiple alignment files**: Select 2 or more pre-aligned sequence files (FASTA, PHYLIP, or NEXUS format)
120 - **Input format**: Specify the format of your input files
121 - **Partition format**: Specify how you want the partition file to be formatted (Unspecified, RAxML, NEXUS)
122 - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences
123 - **Output format**: Select the desired format for the concatenated alignment
124
125 **Outputs**
126
127 1. **Concatenated alignment**: A single file containing all input alignments joined end-to-end
128 2. **Partitions file**: Defines the boundaries of each original alignment within the concatenated file
129
130 @PARTITIONS_HELP@
131
132 **Use cases**
133
134 - **Multi-locus phylogenomics**: Combine hundreds of genes for species tree inference
135 - **Partitioned phylogenetic analysis**: Apply different evolutionary models to different genes using tools like RAxML or IQ-TREE
136 - **Supermatrix construction**: Create dataset for concatenation-based phylogenetic methods
137 - **Increased phylogenetic signal**: Leverage information from multiple loci to resolve difficult nodes
138 - **Comparative analyses**: Prepare datasets for testing hypotheses across multiple genomic regions
139
140 @AMAS_SHARED_HELP@
141 ]]></help>
142
143 <expand macro="citations" />
144 </tool>