--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/seqkit_translate.xml	Fri Mar 29 09:46:24 2024 +0000
@@ -0,0 +1,119 @@
+<tool id="seqkit_translate" name="SeqKit translate" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>Translate nucleotid sequence to protein sequence</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        seqkit translate
+        '$input'
+        -o '$output'
+        #if $translate_or_remove_unknown.selector == 'trimming':
+            $translate_or_remove_unknown.trim
+        #elif $translate_or_remove_unknown.selector == 'translate':
+            $translate_or_remove_unknown.allow_unknown_codon
+        #end if
+        $append_frame
+        $clean
+        #if $frame
+            -f '$frame'
+        #end if
+        $init_codon_as_M
+        #if $transl_table
+            -T '$transl_table'
+        #end if
+
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
+        <param argument="--frame" type="select" multiple="true" label="Frame(s) to translate" >
+            <option value="1" selected="true">1 (default)</option>
+            <option value="2" selected="false">2</option>
+            <option value="3" selected="false">3</option>
+            <option value="-1" selected="false">-1</option>
+            <option value="-2" selected="false">-2</option>
+            <option value="-3" selected="false">-3</option>
+            <option value="6" selected="false">All 6 frames</option>
+        </param>
+        <param argument="--append-frame" type="boolean" truevalue="--append-frame" falsevalue="" checked="false" label="Append frame information to sequence ID ?" />
+        <param argument="--transl-table" type="select" label="Translate table / genetic code to use" >
+            <option value="1" selected="true">1: The Standard Code (default)</option>
+            <option value="2" selected="false">2: The Vertebrate Mitochondrial Code</option>
+            <option value="3" selected="false">3: The Yeast Mitochondrial Code</option>
+            <option value="4" selected="false">4: The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
+            <option value="5" selected="false">5: The Invertebrate Mitochondrial Code</option>
+            <option value="6" selected="false">6: The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
+            <option value="9" selected="false">9: The Echinoderm and Flatworm Mitochondrial Code</option>
+            <option value="10" selected="false">10: The Euplotid Nuclear Code</option>
+            <option value="11" selected="false">11: The Bacterial, Archaeal and Plant Plastid Code</option>
+            <option value="12" selected="false">12: The Alternative Yeast Nuclear Code</option>
+            <option value="13" selected="false">13: The Ascidian Mitochondrial Code</option>
+            <option value="14" selected="false">14: The Alternative Flatworm Mitochondrial Code</option>
+            <option value="16" selected="false">16: Chlorophycean Mitochondrial Code</option>
+            <option value="21" selected="false">21: Trematode Mitochondrial Code</option>
+            <option value="22" selected="false">22: Scenedesmus obliquus Mitochondrial Code</option>
+            <option value="23" selected="false">23: Thraustochytrium Mitochondrial Code</option>
+            <option value="24" selected="false">24: Pterobranchia Mitochondrial Code</option>
+            <option value="25" selected="false">25: Candidate Division SR1 and Gracilibacteria Code</option>
+            <option value="26" selected="false">26: Pachysolen tannophilus Nuclear Code</option>
+            <option value="27" selected="false">27: Karyorelict Nuclear</option>
+            <option value="28" selected="false">28: Condylostoma Nuclear</option>
+            <option value="29" selected="false">29: Mesodinium Nuclear</option>
+            <option value="30" selected="false">30: Peritrich Nuclear</option>
+            <option value="31" selected="false">31: Blastocrithidia Nuclear</option>
+        </param>
+        <param argument="--clean" type="boolean" truevalue="--clean" falsevalue="" checked="false" label="Change all STOP codon positions from the '*' character to 'X' (an unknown residue) ?" />  
+        <conditional name="translate_or_remove_unknown" >
+            <param name="selector" type="select" label="Translate or remove unknown code ?" >
+                <option value="trimming">Remove all 'X' and '*' characters</option>
+                <option value="translate">Translate unknown code to 'X'</option>
+            </param>
+            <when value="trimming">
+                <param argument="--trim" type="boolean" truevalue="--trim" falsevalue="" checked="false" label="Remove all 'X' and '*' characters from the right end of the translation" />
+            </when>
+            <when value="translate">
+                <param argument="--allow-unknown-codon" type="boolean" truevalue="--allow-unknown-codon" falsevalue="" checked="false" label="Translate unknown code to 'X' ?" />
+            </when>
+        </conditional> 
+        <param argument="--init-codon-as-M" type="boolean" truevalue="--init-codon-as-M" falsevalue="" checked="false" label="Translate initial codon at beginning to 'M'" /> 
+    </inputs>
+    <outputs>
+        <data name="output" format_source="input" label="${input.name} translate (${tool.name})"/>
+    </outputs>
+    <tests>
+        <!-- 1. fastq -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <output decompress="true" name="output" file="translate_output3.fastq.gz" ftype="fastqsanger.gz"/>
+        </test>
+        <!-- 2. fasta -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
+            <conditional name="translate_or_remove_unknown">
+                <param name="allow_unknown_codon" value="true"/>
+            </conditional>
+            <param name="append_frame" value="true"/>
+            <param name="clean" value="true"/>
+            <param name="frame" value="2,3" />
+            <param name="init_codon_as_M" value="true" />
+            <param name="transl_table" value="3" />
+            <output decompress="true" name="output" file="translate_output1.fasta.gz" ftype="fasta.gz"/>
+        </test>
+        <!-- 3. fastq + trim -->
+        <test expect_num_outputs="1">
+            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
+            <conditional name="translate_or_remove_unknown">
+                <param name="trim" value="true" />
+            </conditional>
+            <output decompress="true" name="output" file="translate_output2.fastq.gz" ftype="fastqsanger.gz"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Translate DNA/RNA to protein sequence (supporting ambiguous bases)
+
+    </help>
+    <expand macro="citations"/>
+</tool>