diff amas_replicate.xml @ 0:24431ccf6352 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas commit 158ec0e635067d354c425baf14b95cb616fd93c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/amas_replicate.xml	Tue Dec 02 09:26:59 2025 +0000
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+<tool id="amas_replicate" name="AMAS replicate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>replicate 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
+        replicate
+        --rep-aln $replicate_replicates $replicate_loci
+        --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 replicate" 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 replicated alignment(s)" />
+        <param name="replicate_replicates" type="integer" value="10" min="1" label="Number of replicate datasets to build" />
+        <param name="replicate_loci" type="integer" value="2" min="1" label="Number of loci per replicate" />
+        <expand macro="data_type" />
+        <expand macro="check_align" />
+    </inputs>
+
+    <outputs>
+        <expand macro="collection_outputs" name="replicate_alignments" />
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_files" value="inputs/fasta1.fas" />
+            <param name="replicate_replicates" value="2" />
+            <param name="replicate_loci" value="1" />
+            <param name="out_format" value="nexus" />
+            <param name="data_type" value="dna" />
+            <param name="check_align" value="false" />
+            <output_collection name="replicate_alignments_nexus" type="list">
+                <element name="replicate1_1-loci-out.nex" file="outputs/expected_replicate1.nex" ftype="nex" />
+                <element name="replicate2_1-loci-out.nex" file="outputs/expected_replicate2.nex" ftype="nex" />
+            </output_collection>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        **What it does**
+
+        AMAS Replicate generates jackknife or bootstrap replicates by randomly sampling loci (genes) from your dataset. This is used to assess phylogenetic signal distribution and node support across different genomic regions.
+
+        **Inputs**
+
+        - **Alignment files**: Multiple pre-aligned sequence files, one per locus/gene (FASTA, PHYLIP, or NEXUS format)
+        - **Number of replicates**: How many replicate datasets to generate
+        - **Loci per replicate**: How many loci to include in each replicate
+        - **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 replicate alignments
+
+        **Outputs**
+
+        A collection of replicate alignment files. Each replicate contains a random subset of the input loci concatenated together.
+
+        **Use cases**
+
+        - **Phylogenetic jackknifing**: Assess whether phylogenetic signal is driven by specific loci
+        - **Node support evaluation**: Test robustness of tree topology across different gene combinations
+        - **Signal heterogeneity**: Identify whether conflicting signals come from particular genomic regions
+
+        **Example**
+
+        From 100 input genes, create 10 replicates each containing 50 randomly sampled genes. Each replicate can then be used to build a phylogenetic tree, and consistency across replicates indicates robust phylogenetic signal.
+
+        @AMAS_SHARED_HELP@
+    ]]></help>
+
+    <expand macro="citations" />
+</tool>
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