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annotate pal2nal.xml @ 0:a2a40f3bfbbd draft default tip

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planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
author iuc
date Sun, 09 Nov 2025 10:56:06 +0000
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a2a40f3bfbbd planemo upload for repository https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal commit aed49bdc26e503297e1fc394ada087042dc23386
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1 <tool id="pal2nal" name="PAL2NAL" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" profile="24.0">
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2 <description>Codon-based nucleotide alignment from protein and DNA sequences</description>
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4 <macros>
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5 <import>info.xml</import>
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6 <import>macros.xml</import>
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7 <import>tests.xml</import>
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8 </macros>
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10 <expand macro="requirements" />
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12 <expand macro="version_command" />
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14 <expand macro="command" />
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16 <inputs>
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17 <param name="protein_alignment" type="data" format="fasta,clustal" label="Protein alignment"
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18 help="Accepts CLUSTAL/FASTA alignments uploaded through Galaxy." />
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19 <param name="nucleotide_fastas" type="data" format="fasta" multiple="true" min="1"
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20 label="Nucleotide FASTA files" help="Accepts FASTA-formatted nucleotide sequences." />
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22 <param name="output_format" type="select" argument="-output" label="Output format">
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23 <option value="clustal" selected="true">CLUSTAL (default)</option>
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24 <option value="paml">PAML</option>
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25 <option value="fasta">FASTA</option>
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26 <option value="codon">CODON</option>
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27 </param>
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29 <param name="show_only_blocks" type="boolean" argument="-blockonly" truevalue="-blockonly" falsevalue=""
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30 checked="false" label="Show only user-specified blocks" help="Use only '#' marked conserved blocks under CLUSTAL alignment." />
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32 <param name="remove_gaps" type="boolean" argument="-nogap" truevalue="-nogap" falsevalue=""
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33 checked="false" label="Remove codons with gaps or in-frame stop codons" />
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35 <param name="remove_mismatches" type="boolean" argument="-nomismatch" truevalue="-nomismatch" falsevalue=""
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36 checked="false" label="Remove mismatched codons" />
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38 <param name="genetic_code" type="select" argument="-codontable" label="Genetic code">
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39 <option value="1" selected="true">1: Universal</option>
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40 <option value="2">2: Vertebrate mitochondrial</option>
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41 <option value="3">3: Yeast mitochondrial</option>
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42 <option value="4">4: Mold/Protozoan/Coelenterate mito + Mycoplasma</option>
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43 <option value="5">5: Invertebrate mitochondrial</option>
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44 <option value="6">6: Ciliate/Hexamita nuclear</option>
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45 <option value="9">9: Echinoderm/Flatworm mitochondrial</option>
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46 <option value="10">10: Euplotid nuclear</option>
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47 <option value="11">11: Bacterial/Archaeal/Plastid</option>
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48 <option value="12">12: Alternative yeast nuclear</option>
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49 <option value="13">13: Ascidian mitochondrial</option>
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50 <option value="14">14: Alternative flatworm mitochondrial</option>
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51 <option value="15">15: Blepharisma nuclear</option>
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52 <option value="16">16: Chlorophycean mitochondrial</option>
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53 <option value="21">21: Trematode mitochondrial</option>
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54 <option value="22">22: Scenedesmus obliquus mitochondrial</option>
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55 <option value="23">23: Thraustochytrium mitochondrial</option>
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56 </param>
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57
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58 <param name="html_output" type="boolean" truevalue="true" falsevalue=""
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59 checked="false" label="Add HTML formatted output" help="Produce an additional dataset with PAL2NAL's HTML view." />
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61 <param name="suppress_stderr" type="boolean" argument="-nostderr" truevalue="-nostderr" falsevalue=""
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62 checked="false" label="Suppress STDERR messages" help="Hide warning messages (use for automated pipelines)." />
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63 </inputs>
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64
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65 <outputs>
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66 <data name="output_file" format="txt" label="PAL2NAL codon alignment output">
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67 <change_format>
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68 <when input="output_format" value="clustal" format="clustal" />
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69 <when input="output_format" value="fasta" format="fasta" />
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70 <when input="output_format" value="paml" format="phylip" />
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71 <when input="output_format" value="codon" format="txt" />
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72 </change_format>
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73 </data>
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74 <data name="html_output_file" format="html" label="${tool.name} on ${on_string}: HTML view">
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75 <filter>html_output</filter>
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76 </data>
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77 </outputs>
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78
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79 <expand macro="tests" />
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81 <expand macro="help" />
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82
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83 <expand macro="citations" />
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84 </tool>