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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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1 <tool id="amas_summary" name="AMAS summary" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>summarise 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 summary
27 $by_taxon
28 --in-files
29 @INPUT_FILENAMES@
30 --in-format "\${IN_FORMAT}"
31 --data-type $data_type
32 --cores "\${GALAXY_SLOTS:-1}"
33 $check_align
34 ]]></command>
35
36 <inputs>
37 <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequence(s) to summarise" multiple="true"
38 help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." />
39 <param argument="--by-taxon" type="boolean" label="Also emit per-taxon summaries" checked="false" truevalue="--by-taxon" falsevalue="" />
40 <expand macro="data_type" />
41 <expand macro="check_align" />
42 </inputs>
43
44 <outputs>
45 <data name="summary_out" from_work_dir="summary.txt" format="txt" label="${tool.name} on ${on_string}: Alignment summary" />
46
47 <collection name="taxon_summaries" type="list" label="${tool.name} on ${on_string}: Per-taxon summaries">
48 <discover_datasets pattern="(?P&lt;name&gt;.+-seq-summary)\.txt" format="txt" />
49 </collection>
50 </outputs>
51
52 <tests>
53 <test expect_num_outputs="2">
54 <param name="input_files" value="inputs/fasta1.fas" />
55 <param name="by_taxon" value="true" />
56 <param name="data_type" value="dna" />
57 <param name="check_align" value="false" />
58 <output name="summary_out" file="outputs/expected_summary.txt" />
59 <output_collection name="taxon_summaries" type="list">
60 <element name="fasta1.fas-seq-summary" file="outputs/expected_taxa_summary.txt" ftype="txt" />
61 </output_collection>
62 </test>
63 </tests>
64
65 <help><![CDATA[
66 **What it does**
67
68 AMAS Summary calculates comprehensive statistics for sequence alignments, providing quality control metrics essential for phylogenomic analyses.
69
70 **Inputs**
71
72 - **Alignment files**: One or more pre-aligned sequence files (FASTA, PHYLIP, or NEXUS format)
73 - **Input format**: Specify the format of your input files
74 - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences
75 - **Generate per-taxon summaries**: Optionally create detailed statistics for each sequence
76
77 **Outputs**
78
79 1. **Summary table** - Overall statistics for each alignment including:
80 - Number of taxa and alignment length
81 - Total matrix cells and proportion of missing data
82 - Variable sites and parsimony-informative sites
83 - GC content (DNA) or amino acid composition (protein)
84
85 2. **Per-taxon summaries** (optional): Individual statistics for each sequence showing taxon-specific missing data and character frequencies
86
87 **Statistics explained**
88
89 - **Variable sites**: Positions with more than one character state (measures sequence diversity)
90 - **Parsimony-informative sites**: Positions useful for phylogenetic inference (at least 2 taxa share each of 2+ states)
91 - **Missing data**: Proportion of gaps, N's (DNA), or X's (protein)
92 - **Matrix completeness**: Percentage of positions with actual sequence data
93
94 **Use cases**
95
96 - **Quality control**: Identify alignments with excessive missing data
97 - **Alignment comparison**: Compare statistics across multiple genes/loci
98 - **Taxon filtering**: Find sequences with poor coverage
99 - **Publication reporting**: Generate standardized alignment statistics for methods sections
100
101 @AMAS_SHARED_HELP@
102 ]]></help>
103
104 <expand macro="citations" />
105 </tool>