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author cpt
date Fri, 05 Jan 2024 05:51:00 +0000
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1 <tool id="edu.tamu.cpt.fasta.seq_trans" name="Fasta Translate" version="19.1.0.0">
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2 <description>Translate fasta file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 '$__tool_directory__/fasta_translate.py'
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10 @SEQUENCE@
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11
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12 --target '${output.format_select}'
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14 #if str($output.format_select) == "protein":
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15 --table '$output.table'
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16 '$output.strip_stops'
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17 '$output.met'
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18 #end if
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20 > '$default']]></command>
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21 <inputs>
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22 <expand macro="input/fasta"/>
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23 <conditional name="output">
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24 <param label="Target output" type="select" name="format_select">
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25 <option value="rna">RNA</option>
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26 <option value="protein" selected="true">Protein</option>
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27 </param>
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28 <when value="rna"/>
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29 <when value="protein">
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30 <param label="Translation table to use" name="table" type="select">
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31 <option value="1">[1] The Standard Code</option>
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32 <option value="2">[2] The Vertebrate Mitochondrial Code</option>
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33 <option value="3">[3] The Yeast Mitochondrial Code</option>
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34 <option value="4">[4] The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
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35 <option value="5">[5] The Invertebrate Mitochondrial Code </option>
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36 <option value="6">[6] The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
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37 <option value="9">[9] The Echinoderm and Flatworm Mitochondrial Code</option>
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38 <option value="10">[10] The Euplotid Nuclear Code</option>
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39 <option value="11" selected="true">[11] The Bacterial, Archaeal and Plant Plastid Code</option>
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40 <option value="12">[12] The Alternative Yeast Nuclear Code</option>
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41 <option value="13">[13] The Ascidian Mitochondrial Code</option>
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42 <option value="14">[14] The Alternative Flatworm Mitochondrial Code</option>
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43 <option value="15">[15] Blepharisma Nuclear Code</option>
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44 <option value="16">[16] Chlorophycean Mitochondrial Code</option>
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45 <option value="21">[21] Trematode Mitochondrial Code</option>
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46 <option value="22">[22] Scenedesmus Obliquus Mitochondrial Code</option>
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47 <option value="23">[23] Thraustochytrium Mitochondrial Code</option>
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48 <option value="24">[24] Pterobranchia Mitochondrial Code</option>
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49 <option value="25">[25] Candidate Division SR1 and Gracilibacteria Code</option>
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50 </param>
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51 <param label="Remove stop characters" name="strip_stops" type="boolean" checked="true" truevalue="--strip_stops" falsevalue=""/>
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52 <param label="Convert first residue to Met" name="met" type="boolean" checked="false" truevalue="--met" falsevalue=""/>
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53 </when>
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54 </conditional>
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55 </inputs>
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56 <outputs>
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57 <data format="fasta" hidden="false" name="default"/>
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="sequences" value="T7_TranslateIn.fasta"/>
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62 <param name="format_select" value="protein"/>
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63 <param name="table" value="11"/>
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64 <param name="strip_stops" value="--strip_stops"/>
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65 <output name="default" file="T7_TranslateOut.fasta"/>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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69 **What it does**
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70
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71 Translate DNA sequences from an input FASTA or multi-FASTA file to protein or RNA sequences, as selected.
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72 ]]></help>
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73 <expand macro="citations"/>
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74 </tool>