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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 09:26:31 +0000
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5e15238e9e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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1 <tool id="amas_summary" name="AMAS summary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>summarise 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 summary
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27 $by_taxon
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28 --in-files
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29 @INPUT_FILENAMES@
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30 --in-format "\${IN_FORMAT}"
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31 --data-type $data_type
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32 --cores "\${GALAXY_SLOTS:-1}"
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33 $check_align
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34 ]]></command>
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35
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36 <inputs>
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37 <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequence(s) to summarise" multiple="true"
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38 help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." />
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39 <param argument="--by-taxon" type="boolean" label="Also emit per-taxon summaries" checked="false" truevalue="--by-taxon" falsevalue="" />
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40 <expand macro="data_type" />
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41 <expand macro="check_align" />
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42 </inputs>
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43
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44 <outputs>
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45 <data name="summary_out" from_work_dir="summary.txt" format="txt" label="${tool.name} on ${on_string}: Alignment summary" />
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47 <collection name="taxon_summaries" type="list" label="${tool.name} on ${on_string}: Per-taxon summaries">
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48 <discover_datasets pattern="(?P&lt;name&gt;.+-seq-summary)\.txt" format="txt" />
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49 </collection>
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50 </outputs>
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51
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52 <tests>
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53 <test expect_num_outputs="2">
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54 <param name="input_files" value="inputs/fasta1.fas" />
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55 <param name="by_taxon" value="true" />
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56 <param name="data_type" value="dna" />
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57 <param name="check_align" value="false" />
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58 <output name="summary_out" file="outputs/expected_summary.txt" />
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59 <output_collection name="taxon_summaries" type="list">
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60 <element name="fasta1.fas-seq-summary" file="outputs/expected_taxa_summary.txt" ftype="txt" />
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61 </output_collection>
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62 </test>
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63 </tests>
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64
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65 <help><![CDATA[
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66 **What it does**
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67
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68 AMAS Summary calculates comprehensive statistics for sequence alignments, providing quality control metrics essential for phylogenomic analyses.
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69
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70 **Inputs**
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71
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72 - **Alignment files**: One or more pre-aligned sequence files (FASTA, PHYLIP, or NEXUS format)
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73 - **Input format**: Specify the format of your input files
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74 - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences
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75 - **Generate per-taxon summaries**: Optionally create detailed statistics for each sequence
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76
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77 **Outputs**
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79 1. **Summary table** - Overall statistics for each alignment including:
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80 - Number of taxa and alignment length
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81 - Total matrix cells and proportion of missing data
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82 - Variable sites and parsimony-informative sites
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83 - GC content (DNA) or amino acid composition (protein)
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84
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85 2. **Per-taxon summaries** (optional): Individual statistics for each sequence showing taxon-specific missing data and character frequencies
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86
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87 **Statistics explained**
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88
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89 - **Variable sites**: Positions with more than one character state (measures sequence diversity)
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90 - **Parsimony-informative sites**: Positions useful for phylogenetic inference (at least 2 taxa share each of 2+ states)
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91 - **Missing data**: Proportion of gaps, N's (DNA), or X's (protein)
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92 - **Matrix completeness**: Percentage of positions with actual sequence data
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93
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94 **Use cases**
5e15238e9e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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96 - **Quality control**: Identify alignments with excessive missing data
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97 - **Alignment comparison**: Compare statistics across multiple genes/loci
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98 - **Taxon filtering**: Find sequences with poor coverage
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99 - **Publication reporting**: Generate standardized alignment statistics for methods sections
5e15238e9e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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101 @AMAS_SHARED_HELP@
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102 ]]></help>
5e15238e9e55 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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104 <expand macro="citations" />
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105 </tool>