Mercurial > repos > iuc > amas_replicate

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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 09:25:30 +0000
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1 <tool id="amas_replicate" name="AMAS replicate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>replicate 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[
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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 replicate
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27 --rep-aln $replicate_replicates $replicate_loci
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28 --out-format $out_format
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29 --in-files
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30 @INPUT_FILENAMES@
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31 --in-format "\${IN_FORMAT}"
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32 --data-type $data_type
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33 --cores "\${GALAXY_SLOTS:-1}"
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34 $check_align
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35 ]]></command>
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36
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37 <inputs>
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38 <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequence(s) to replicate" multiple="true"
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39 help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." />
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40 <expand macro="output_format" label="Select output format for replicated alignment(s)" />
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41 <param name="replicate_replicates" type="integer" value="10" min="1" label="Number of replicate datasets to build" />
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42 <param name="replicate_loci" type="integer" value="2" min="1" label="Number of loci per replicate" />
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43 <expand macro="data_type" />
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44 <expand macro="check_align" />
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45 </inputs>
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46
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47 <outputs>
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48 <expand macro="collection_outputs" name="replicate_alignments" />
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49 </outputs>
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51 <tests>
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52 <test expect_num_outputs="1">
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53 <param name="input_files" value="inputs/fasta1.fas" />
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54 <param name="replicate_replicates" value="2" />
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55 <param name="replicate_loci" value="1" />
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56 <param name="out_format" value="nexus" />
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57 <param name="data_type" value="dna" />
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58 <param name="check_align" value="false" />
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59 <output_collection name="replicate_alignments_nexus" type="list">
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60 <element name="replicate1_1-loci-out.nex" file="outputs/expected_replicate1.nex" ftype="nex" />
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61 <element name="replicate2_1-loci-out.nex" file="outputs/expected_replicate2.nex" ftype="nex" />
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62 </output_collection>
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63 </test>
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64 </tests>
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65
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66 <help><![CDATA[
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67 **What it does**
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68
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69 AMAS Replicate generates jackknife or bootstrap replicates by randomly sampling loci (genes) from your dataset. This is used to assess phylogenetic signal distribution and node support across different genomic regions.
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70
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71 **Inputs**
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72
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73 - **Alignment files**: Multiple pre-aligned sequence files, one per locus/gene (FASTA, PHYLIP, or NEXUS format)
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74 - **Number of replicates**: How many replicate datasets to generate
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75 - **Loci per replicate**: How many loci to include in each replicate
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76 - **Input format**: Specify the format of your input files
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77 - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences
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78 - **Output format**: Select the desired format for the replicate alignments
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79
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80 **Outputs**
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81
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82 A collection of replicate alignment files. Each replicate contains a random subset of the input loci concatenated together.
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83
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84 **Use cases**
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85
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86 - **Phylogenetic jackknifing**: Assess whether phylogenetic signal is driven by specific loci
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87 - **Node support evaluation**: Test robustness of tree topology across different gene combinations
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88 - **Signal heterogeneity**: Identify whether conflicting signals come from particular genomic regions
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89
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90 **Example**
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91
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92 From 100 input genes, create 10 replicates each containing 50 randomly sampled genes. Each replicate can then be used to build a phylogenetic tree, and consistency across replicates indicates robust phylogenetic signal.
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93
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94 @AMAS_SHARED_HELP@
4fabfa5ff38c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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95 ]]></help>
4fabfa5ff38c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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96
4fabfa5ff38c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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97 <expand macro="citations" />
4fabfa5ff38c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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98 </tool>