--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/remove_terminal_stop_codons.xml	Fri Dec 05 23:22:22 2025 +0000
@@ -0,0 +1,151 @@
+<tool id="remove_terminal_stop_codons" name="Remove terminal stop codons" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>from coding sequences</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">25.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="1.84">biopython</requirement>
+    </requirements>
+    <required_files>
+        <include path="remove_terminal_stop_codons.py" />
+    </required_files>
+    <command detect_errors="exit_code"><![CDATA[
+        python '$__tool_directory__/remove_terminal_stop_codons.py'
+            -i '$input'
+            -o '$output'
+            #if str($genetic_code) != "1"
+                -t '$genetic_code'
+            #end if
+            $no_check_internal
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Input FASTA file"
+            help="FASTA file containing coding sequences (CDS) to process." />
+        <param name="genetic_code" type="select" label="Genetic code"
+            help="NCBI translation table to use for identifying stop codons. Different organisms use different genetic codes.">
+            <option value="1" selected="true">1 - Standard</option>
+            <option value="2">2 - Vertebrate Mitochondrial</option>
+            <option value="3">3 - Yeast Mitochondrial</option>
+            <option value="4">4 - Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma</option>
+            <option value="5">5 - Invertebrate Mitochondrial</option>
+            <option value="6">6 - Ciliate, Dasycladacean and Hexamita Nuclear</option>
+            <option value="9">9 - Echinoderm and Flatworm Mitochondrial</option>
+            <option value="10">10 - Euplotid Nuclear</option>
+            <option value="11">11 - Bacterial, Archaeal and Plant Plastid</option>
+            <option value="12">12 - Alternative Yeast Nuclear</option>
+            <option value="13">13 - Ascidian Mitochondrial</option>
+            <option value="14">14 - Alternative Flatworm Mitochondrial</option>
+            <option value="15">15 - Blepharisma Nuclear</option>
+            <option value="16">16 - Chlorophycean Mitochondrial</option>
+            <option value="21">21 - Trematode Mitochondrial</option>
+            <option value="22">22 - Scenedesmus obliquus Mitochondrial</option>
+            <option value="23">23 - Thraustochytrium Mitochondrial</option>
+            <option value="24">24 - Rhabdopleuridae Mitochondrial</option>
+            <option value="25">25 - Candidate Division SR1 and Gracilibacteria</option>
+            <option value="26">26 - Pachysolen tannophilus Nuclear</option>
+            <option value="27">27 - Karyorelict Nuclear</option>
+            <option value="28">28 - Condylostoma Nuclear</option>
+            <option value="29">29 - Mesodinium Nuclear</option>
+            <option value="30">30 - Peritrich Nuclear</option>
+            <option value="31">31 - Blastocrithidia Nuclear</option>
+            <option value="33">33 - Cephalodiscidae Mitochondrial UAA-Tyr</option>
+        </param>
+        <param argument="--no-check-internal" type="boolean" truevalue="--no-check-internal" falsevalue=""
+            checked="false" label="Skip internal stop codon check"
+            help="By default, the tool will fail if internal (in-frame) stop codons are found. Enable this to only remove terminal stops without checking for internal ones." />
+    </inputs>
+    <outputs>
+        <data name="output" format="fasta" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <!-- Test 1: Basic removal of terminal stop codon -->
+        <test expect_num_outputs="1">
+            <param name="input" value="with_terminal_stop.fasta" ftype="fasta" />
+            <param name="genetic_code" value="1" />
+            <output name="output" file="without_terminal_stop.fasta" ftype="fasta" />
+        </test>
+        <!-- Test 2: Sequence without terminal stop (should pass through unchanged) -->
+        <test expect_num_outputs="1">
+            <param name="input" value="no_terminal_stop.fasta" ftype="fasta" />
+            <param name="genetic_code" value="1" />
+            <output name="output" file="no_terminal_stop.fasta" ftype="fasta" />
+        </test>
+        <!-- Test 3: Internal stop codon should fail -->
+        <test expect_failure="true">
+            <param name="input" value="with_internal_stop.fasta" ftype="fasta" />
+            <param name="genetic_code" value="1" />
+        </test>
+        <!-- Test 4: Internal stop with skip check should pass -->
+        <test expect_num_outputs="1">
+            <param name="input" value="with_internal_stop.fasta" ftype="fasta" />
+            <param name="genetic_code" value="1" />
+            <param name="no_check_internal" value="true" />
+            <output name="output" file="with_internal_stop_output.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This tool removes terminal (trailing) stop codons from coding sequences in a FASTA file.
+It is designed as a **preprocessing step** for downstream tools like **cawlign** and **HyPhy**
+that do not permit stop codons in their input sequences.
+
+**Important**: By default, this tool will **fail with an error** if it detects any internal
+(in-frame) stop codons in your sequences. This is intentional, but can be disabled with the
+`--no-check-internal` option.
+
+----
+
+**Input**
+
+A FASTA file containing coding sequences (CDS). Sequences should be:
+
+- In the correct reading frame (starting at position 1 of a codon)
+- DNA sequences (RNA sequences with U will be converted to T)
+
+----
+
+**Output**
+
+A FASTA file with terminal stop codons removed. The output preserves:
+
+- Sequence identifiers and descriptions
+- Sequences that don't end with stop codons (passed through unchanged)
+- Partial codons at the end (not removed)
+
+----
+
+**Genetic Codes**
+
+Different organisms use different genetic codes (translation tables) which define
+which codons are stop codons:
+
+- **Standard (1)**: TAA, TAG, TGA - used by most organisms
+- **Vertebrate Mitochondrial (2)**: TAA, TAG, AGA, AGG - mitochondria of vertebrates
+- **Bacterial/Archaeal (11)**: TAA, TAG, TGA - bacteria and archaea
+
+Select the appropriate genetic code for your organism to ensure correct stop codon identification.
+
+----
+
+**Use Cases**
+
+1. **Before cawlign**: Remove terminal stops from sequences before codon-aware alignment
+2. **Before HyPhy**: Prepare sequences for selection analysis (HyPhy methods like BUSTED, FEL, MEME)
+3. **Quality control**: Identify sequences with internal stop codons that may need review
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{capheine2025,
+    author = {Callan, Danielle and Verdonk, Hannah and Kosakovsky Pond, Sergei L.},
+    title = {CAPHEINE: A Comprehensive Automated Pipeline Using HyPhy for Evolutionary Inference with Nextflow},
+    year = {2025},
+    publisher = {GitHub},
+    url = {https://github.com/veg/CAPHEINE},
+    note = {Terminal stop-codon removal logic in this Galaxy tool is adapted from the CAPHEINE pipeline.}
+}
+        </citation>
+    </citations>
+</tool>