Mercurial > repos > iuc > amas_remove

comparison amas_remove.xml @ 0:63224da0018f draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
author iuc
date Tue, 02 Dec 2025 09:25:46 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:63224da0018f
1 <tool id="amas_remove" name="AMAS remove" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>remove taxa from 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 remove
27 --taxa-to-remove
28 #for $taxon in $taxa_to_remove.split()
29 '$taxon'
30 #end for
31 --out-format $out_format
32 --in-files
33 @INPUT_FILENAMES@
34 --in-format "\${IN_FORMAT}"
35 --data-type $data_type
36 --cores "\${GALAXY_SLOTS:-1}"
37 $check_align
38 ]]></command>
39
40 <inputs>
41 <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequence(s) to remove taxa" multiple="true"
42 help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." />
43 <expand macro="output_format" label="Select output format for alignment(s) with taxa removed"/>
44 <param name="taxa_to_remove" type="text" label="Taxa to remove"
45 help="Space-separated list of taxon names to remove (e.g., 'OTU9 OTU10 Sample_A'). Note: AMAS converts spaces to underscores and strips quotes from sequence names, so use 'Species_1' to remove a taxon named 'Species 1'.">
46 <validator type="regex" message="Please provide at least one taxon name (alphanumeric, underscores, hyphens, and dots allowed)">[A-Za-z0-9_.\-]+(\s+[A-Za-z0-9_.\-]+)*</validator>
47 </param>
48 <expand macro="data_type" />
49 <expand macro="check_align" />
50 </inputs>
51
52 <outputs>
53 <expand macro="collection_outputs" name="reduced_alignments" />
54 </outputs>
55
56 <tests>
57 <test expect_num_outputs="1">
58 <param name="input_files" value="inputs/remove_input.nex" />
59 <param name="taxa_to_remove" value="OTU9 OTU10" />
60 <param name="out_format" value="nexus-int" />
61 <param name="data_type" value="dna" />
62 <param name="check_align" value="false" />
63 <output_collection name="reduced_alignments_nexus" type="list">
64 <element name="reduced_remove_input.nex-out.int-nex" file="outputs/expected_remove_filtered.int-nex" ftype="nex" />
65 </output_collection>
66 </test>
67 </tests>
68
69 <help><![CDATA[
70 **What it does**
71
72 AMAS Remove excludes specified taxa (sequences) from one or more alignments. This is useful for removing problematic sequences, outgroups, or creating taxon subsets for comparative analyses.
73
74 **Inputs**
75
76 - **Alignment files**: One or more pre-aligned sequence files (FASTA, PHYLIP, or NEXUS format)
77 - **Taxa to remove**: Space-separated list of sequence names to exclude (e.g., 'OTU9 OTU10 Sample_A')
78
79 **Important**: AMAS converts spaces to underscores and strips quotes from sequence names during processing. If your input file contains a taxon named 'Species 1' or '"Species 1"', you must specify it as 'Species_1' in the taxa to remove list.
80
81 - **Input format**: Specify the format of your input files
82 - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences
83 - **Output format**: Select the desired format for the reduced alignments
84
85 **Outputs**
86
87 A collection of alignment files with specified taxa removed. Each output file contains the same alignment as the input, minus the excluded sequences.
88
89 **Tip:** You may want to realign your files after taxon removal.
90
91 **Use cases**
92
93 - Remove sequences with excessive missing data
94 - Exclude contaminated or mis-identified samples
95 - Create taxon subsets for sensitivity analyses
96 - Remove outgroups after tree rooting
97
98 @AMAS_SHARED_HELP@
99 ]]></help>
100
101 <expand macro="citations" />
102 </tool>