--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/amas_remove.xml	Tue Dec 02 09:25:46 2025 +0000
@@ -0,0 +1,102 @@
+<tool id="amas_remove" name="AMAS remove" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>remove taxa from multiple alignments</description>
+    
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+
+    <xrefs>
+        <xref type="bio.tools">amas</xref>
+    </xrefs>
+
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+        set -eu;
+
+        @SNIFF_INPUT_FORMAT@
+
+        @CHECK_INTERLEAVED@
+
+        @SYMLINK_INPUTS@
+
+        python -m amas.AMAS
+        remove
+        --taxa-to-remove
+        #for $taxon in $taxa_to_remove.split()
+            '$taxon'
+        #end for
+        --out-format $out_format
+        --in-files
+            @INPUT_FILENAMES@
+        --in-format "\${IN_FORMAT}"
+        --data-type $data_type
+        --cores "\${GALAXY_SLOTS:-1}"
+        $check_align
+    ]]></command>
+
+    <inputs>
+        <param name="input_files" type="data" format="fasta,phylip,nex" label="Sequence(s) to remove taxa" multiple="true" 
+               help="Provide pre-aligned FASTA/PHYLIP/NEXUS files (DNA or protein); mixes of unaligned reads or contigs will produce meaningless results." />
+        <expand macro="output_format" label="Select output format for alignment(s) with taxa removed"/>
+        <param name="taxa_to_remove" type="text" label="Taxa to remove" 
+               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'.">
+            <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>
+        </param>
+        <expand macro="data_type" />
+        <expand macro="check_align" />
+    </inputs>
+
+    <outputs>
+        <expand macro="collection_outputs" name="reduced_alignments" />
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_files" value="inputs/remove_input.nex" />
+            <param name="taxa_to_remove" value="OTU9 OTU10" />
+            <param name="out_format" value="nexus-int" />
+            <param name="data_type" value="dna" />
+            <param name="check_align" value="false" />
+            <output_collection name="reduced_alignments_nexus" type="list">
+                <element name="reduced_remove_input.nex-out.int-nex" file="outputs/expected_remove_filtered.int-nex" ftype="nex" />
+            </output_collection>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        **What it does**
+
+        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.
+
+        **Inputs**
+
+        - **Alignment files**: One or more pre-aligned sequence files (FASTA, PHYLIP, or NEXUS format)
+        - **Taxa to remove**: Space-separated list of sequence names to exclude (e.g., 'OTU9 OTU10 Sample_A')
+        
+        **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.
+        
+        - **Input format**: Specify the format of your input files
+        - **Data type**: Choose DNA for nucleotide sequences or Protein for amino acid sequences
+        - **Output format**: Select the desired format for the reduced alignments
+
+        **Outputs**
+
+        A collection of alignment files with specified taxa removed. Each output file contains the same alignment as the input, minus the excluded sequences.
+
+        **Tip:** You may want to realign your files after taxon removal.
+
+        **Use cases**
+
+        - Remove sequences with excessive missing data
+        - Exclude contaminated or mis-identified samples
+        - Create taxon subsets for sensitivity analyses
+        - Remove outgroups after tree rooting
+
+        @AMAS_SHARED_HELP@
+    ]]></help>
+
+    <expand macro="citations" />
+</tool>
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