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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 09:26:16 +0000
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b7e4e1487fc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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1 <tool id="amas_split" name="AMAS split" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>split multiple alignments</description>
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3
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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[
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16 #import re
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17 set -eu;
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19 ## Let galaxy sniff input format
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20 #set $in_format = $input_file.ext
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21 #if $in_format == 'nex'
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22 #set $in_format = 'nexus'
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23 #end if
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25 ## Check if inputs are interleaved
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26 IN_FORMAT=\$(python '$__tool_directory__/check_interleaved.py'
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27 '${input_file}'
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28 --format '${in_format}') &&
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29
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30 ## Create symlinks with original filename for consistent tests because
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31 ## input filenames are used as str vars
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32 #set $safename_input = re.sub('[^\w\-_\.]', '_', $input_file.element_identifier)
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33 ln -s '${input_file}' '${safename_input}';
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34
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35 python -m amas.AMAS
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36 split
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37 --split-by $split_by
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38 $remove_empty
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39 --out-format $out_format
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40 --in-files $safename_input
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41 --in-format "\${IN_FORMAT}"
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42 --data-type $data_type
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43 --cores "\${GALAXY_SLOTS:-1}"
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44 $check_align
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45 ]]></command>
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46
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47 <inputs>
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48 <param name="input_file" type="data" format="fasta,phylip,nex" label="Sequence to split" multiple="false" help="Provide pre-aligned FASTA/PHYLIP/NEXUS file (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." />
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49 <expand macro="output_format" label="Select output format for split alignments" />
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50 <!-- If amas updates split to handle NEXUS format include nex format here -->
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51 <param name="split_by" type="data" format="txt" label="Partitions file for splitting. Note: needs to be a partions file in the Unspecified format (See help section for more information)"
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52 help="A file defining how to split the concatenated alignment into separate gene/locus regions. Each line specifies a partition name and its position range (e.g., 'gene1 = 1-500' for unspecified format). See the help section for more information about partitions." />
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53 <param argument="--remove-empty" type="boolean" label="Remove taxa that are entirely missing within a partition" checked="false" truevalue="--remove-empty" falsevalue="" />
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54 <expand macro="data_type" />
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55 <expand macro="check_align" />
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56 </inputs>
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57
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58 <outputs>
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59 <expand macro="collection_outputs" name="split_alignments" />
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60 </outputs>
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61
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62 <tests>
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63 <test expect_num_outputs="1">
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64 <param name="input_file" value="inputs/concat_result.phylip" />
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65 <param name="split_by" value="inputs/partitions_concat_unspecified.txt" />
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66 <param name="remove_empty" value="true" />
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67 <param name="out_format" value="fasta" />
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68 <param name="data_type" value="dna" />
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69 <param name="check_align" value="false" />
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70 <output_collection name="split_alignments_fasta" type="list">
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71 <element name="concat_result_p1_concat_1-out.fas" file="outputs/expected_split_partition1.fas" ftype="fasta" />
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72 <element name="concat_result_p2_concat_2-out.fas" file="outputs/expected_split_partition2.fas" ftype="fasta" />
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73 </output_collection>
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74 </test>
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75 </tests>
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76
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77 <help><![CDATA[
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78 **What it does**
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79
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80 AMAS Split divides a concatenated alignment back into separate gene/locus files using a partitions file. This is the reverse operation of AMAS Concat.
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81
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82 **Inputs**
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83
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84 - **Concatenated alignment**: A single alignment file containing multiple genes/loci joined end-to-end
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85 - **Partitions file**: Defines the boundaries of each gene/locus (.txt file containing Unspecified formatting)
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86 - **Input format**: Specify the format of your concatenated alignment
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87 - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences
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88 - **Output format**: Select the desired format for the split alignment files
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89 - **Remove empty sequences**: Optionally exclude taxa with only gaps/missing data in a partition
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90
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91 **Outputs**
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92
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93 A collection of alignment files, one per partition/gene defined in your partitions file.
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94
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95 @PARTITIONS_HELP@
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96
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97 **IMPORTANT**: A .txt file containing RAxML, or NEXUS formatting, or a .nex file containing NEXUS formatting that are produced using AMAS Concat will not work.
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98
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99 **Tip:** An example for your data can be generated using the AMAS concat tool.
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100
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101 **Use cases**
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102
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103 - Extract individual gene alignments from a concatenated dataset
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104 - Analyze genes separately after joint phylogenetic analysis
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105 - Apply gene-specific filtering or trimming
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106 - Recover original locus alignments from published concatenated datasets
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107
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108 @AMAS_SHARED_HELP@
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109 ]]></help>
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111 <expand macro="citations" />
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112 </tool>