Mercurial > repos > iuc > amas_remove

annotate amas_remove.xml @ 0:fefe2c3755f4 draft default tip

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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 09:27:20 +0000
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fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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1 <tool id="amas_remove" name="AMAS remove" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>remove taxa from 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 remove
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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27 --taxa-to-remove
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28 #for $taxon in $taxa_to_remove.split()
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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29 '$taxon'
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30 #end for
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31 --out-format $out_format
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32 --in-files
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33 @INPUT_FILENAMES@
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34 --in-format "\${IN_FORMAT}"
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35 --data-type $data_type
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36 --cores "\${GALAXY_SLOTS:-1}"
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37 $check_align
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38 ]]></command>
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39
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40 <inputs>
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41 <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequence(s) to remove taxa" multiple="true"
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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42 help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." />
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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43 <expand macro="output_format" label="Select output format for alignment(s) with taxa removed"/>
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44 <param name="taxa_to_remove" type="text" label="Taxa to remove"
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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'.">
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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>
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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47 </param>
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48 <expand macro="data_type" />
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49 <expand macro="check_align" />
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50 </inputs>
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51
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52 <outputs>
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53 <expand macro="collection_outputs" name="reduced_alignments" />
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54 </outputs>
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55
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56 <tests>
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57 <test expect_num_outputs="1">
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58 <param name="input_files" value="inputs/remove_input.nex" />
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59 <param name="taxa_to_remove" value="OTU9 OTU10" />
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60 <param name="out_format" value="nexus-int" />
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61 <param name="data_type" value="dna" />
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62 <param name="check_align" value="false" />
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63 <output_collection name="reduced_alignments_nexus" type="list">
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64 <element name="reduced_remove_input.nex-out.int-nex" file="outputs/expected_remove_filtered.int-nex" ftype="nex" />
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65 </output_collection>
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66 </test>
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67 </tests>
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68
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69 <help><![CDATA[
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70 **What it does**
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71
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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.
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73
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74 **Inputs**
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75
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76 - **Alignment files**: One or more pre-aligned sequence files (FASTA, PHYLIP, or NEXUS format)
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77 - **Taxa to remove**: Space-separated list of sequence names to exclude (e.g., 'OTU9 OTU10 Sample_A')
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78
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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.
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80
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81 - **Input format**: Specify the format of your input files
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82 - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences
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83 - **Output format**: Select the desired format for the reduced alignments
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84
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85 **Outputs**
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86
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87 A collection of alignment files with specified taxa removed. Each output file contains the same alignment as the input, minus the excluded sequences.
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88
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89 **Tip:** You may want to realign your files after taxon removal.
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90
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91 **Use cases**
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92
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93 - Remove sequences with excessive missing data
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94 - Exclude contaminated or mis-identified samples
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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95 - Create taxon subsets for sensitivity analyses
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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96 - Remove outgroups after tree rooting
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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97
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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98 @AMAS_SHARED_HELP@
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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99 ]]></help>
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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100
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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101 <expand macro="citations" />
fefe2c3755f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4
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102 </tool>