--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_translate.xml	Mon Jun 05 02:41:52 2023 +0000
@@ -0,0 +1,74 @@
+<tool id="edu.tamu.cpt.fasta.seq_trans" name="Fasta Translate" version="19.1.0.0">
+    <description>Translate fasta file</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>cpt-macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="aggressive"><![CDATA[
+'$__tool_directory__/fasta_translate.py'
+@SEQUENCE@
+
+--target '${output.format_select}'
+
+#if str($output.format_select) == "protein":
+		--table '$output.table'
+		'$output.strip_stops'
+		'$output.met'
+#end if
+
+> '$default']]></command>
+    <inputs>
+        <expand macro="input/fasta"/>
+        <conditional name="output">
+            <param label="Target output" type="select" name="format_select">
+                <option value="rna">RNA</option>
+                <option value="protein" selected="true">Protein</option>
+            </param>
+            <when value="rna"/>
+            <when value="protein">
+                <param label="Translation table to use" name="table" type="select">
+                    <option value="1">[1] The Standard Code</option>
+                    <option value="2">[2] The Vertebrate Mitochondrial Code</option>
+                    <option value="3">[3] The Yeast Mitochondrial Code</option>
+                    <option value="4">[4] The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
+                    <option value="5">[5] The Invertebrate Mitochondrial Code </option>
+                    <option value="6">[6] The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
+                    <option value="9">[9] The Echinoderm and Flatworm Mitochondrial Code</option>
+                    <option value="10">[10] The Euplotid Nuclear Code</option>
+                    <option value="11" selected="true">[11] The Bacterial, Archaeal and Plant Plastid Code</option>
+                    <option value="12">[12] The Alternative Yeast Nuclear Code</option>
+                    <option value="13">[13] The Ascidian Mitochondrial Code</option>
+                    <option value="14">[14] The Alternative Flatworm Mitochondrial Code</option>
+                    <option value="15">[15] Blepharisma Nuclear Code</option>
+                    <option value="16">[16] Chlorophycean Mitochondrial Code</option>
+                    <option value="21">[21] Trematode Mitochondrial Code</option>
+                    <option value="22">[22] Scenedesmus Obliquus Mitochondrial Code</option>
+                    <option value="23">[23] Thraustochytrium Mitochondrial Code</option>
+                    <option value="24">[24] Pterobranchia Mitochondrial Code</option>
+                    <option value="25">[25] Candidate Division SR1 and Gracilibacteria Code</option>
+                </param>
+                <param label="Remove stop characters" name="strip_stops" type="boolean" checked="true" truevalue="--strip_stops" falsevalue=""/>
+                <param label="Convert first residue to Met" name="met" type="boolean" checked="false" truevalue="--met" falsevalue=""/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="fasta" hidden="false" name="default"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="sequences" value="T7_TranslateIn.fasta"/>
+            <param name="format_select" value="protein"/>
+            <param name="table" value="11"/>
+            <param name="strip_stops" value="--strip_stops"/>
+            <output name="default" file="T7_TranslateOut.fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+Translate DNA sequences from an input FASTA or multi-FASTA file to protein or RNA sequences, as selected. 
+]]></help>
+    <expand macro="citations"/>
+</tool>