Mercurial > repos > iuc > squirrel_phylo

annotate squirrel-phylo.xml @ 3:46a0e11a7607 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel commit 68ea06281ba78b828b8d1947745161697dc0fbc5
author iuc
date Tue, 10 Jun 2025 13:32:43 +0000
parents eaa0b1e114eb
children
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b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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1 <tool id="squirrel_phylo" name="Squirrel Phylo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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2 <description>Phylogenetic and APOBEC3 analysis of MPXV (Mpox virus)</description>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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3 <macros>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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4 <import>macros.xml</import>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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5 </macros>
1
eaa0b1e114eb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel commit d684b71bf5129645fe8eb349a56fcb29c321a7ab
iuc
parents: 0
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6 <expand macro="xrefs"/>
0
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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7 <expand macro="requirements"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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8 <expand macro="version_command"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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10 <command detect_errors="exit_code"><![CDATA[
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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11 #set $alignment_output = 'input.aln.fasta'
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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12 #set $tree_output = 'input.tree'
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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13
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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14 #if $apobec3
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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15 #set $aa_recon_output = "input.tree.amino_acid.reconstruction.csv"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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16 #set $branch_snps_output = "input.tree.branch_snps.reconstruction.csv"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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17 #set $svg_output = "input.tree.svg"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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18 #set $png_output = "input.tree.png"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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19 #end if
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b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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21 ln -s '${sequences}' input.fasta &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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23 squirrel
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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24 #if $apobec3
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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25 --run-apobec3-phylo
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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26 --fig-height $fig_height
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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27 --fig-width $fig_width
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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28 #else
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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29 --run-phylo
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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30 #end if
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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31
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32 --clade $clade
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33
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34 #if $mask_file
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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35 --additional-mask $mask_file
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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36 #end if
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37
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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38 #if $bg_file
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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39 --background-file '$bg_file'
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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40 #else
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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41 --include-background
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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42 #end if
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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43
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44 #if $out_group
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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45 --outgroups $out_group
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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46 #end if
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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47
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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48 $no_mask
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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49 $no_iter_mask
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50
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51 --threads \${GALAXY_SLOTS:-1}
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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52 input.fasta &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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53
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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54 mv '${alignment_output}' '$alignment' &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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55 mv '${tree_output}' '$tree'
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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56
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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57 #if $apobec3
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58 && mv '${aa_recon_output}' '$aa_recon' &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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59 mv '${branch_snps_output}' '$branch_snps' &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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60 mv '${svg_output}' '$svg' &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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61 mv '${png_output}' '$png'
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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62 #end if
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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63 ]]></command>
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64
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65 <inputs>
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66 <param name="sequences"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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67 type="data"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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68 format="fasta"
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69 label="Sequences in fasta format"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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70 help="You can upload a FASTA sequence to the history and use it as reference" />
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71 <param name="apobec3"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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72 type="boolean"
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73 checked="false"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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74 label="Run additional APOBEC3-mutation reconstruction pipeline" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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75 <param name="clade"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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76 type="select"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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77 label="Select MPXV Clade">
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78 <option value="cladei">Clade I</option>
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79 <option value="cladeia">Clade Ia</option>
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80 <option value="cladeib">Clade Ib</option>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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81 <option value="cladeii">Clade II</option>
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82 <option value="cladeiia">Clade IIa</option>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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83 <option value="cladeiib">Clade IIb</option>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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84 </param>
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85 <section name="other_settings" expanded="false" title="Additional Settings">
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86 <param name="no_mask"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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87 type="boolean"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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88 truevalue="--no-mask"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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89 falsevalue=""
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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90 label="SKIP masking repeat regions?"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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91 help="Set to True to Skip masking of repetitive regions. Default: masks repeat regions." />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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92 <param name="no_iter_mask"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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93 type="boolean"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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94 truevalue="--no-itr-mask"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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95 falsevalue=""
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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96 label="SKIP masking of end ITR?"
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97 help="Set to True to skip masking of end ITR. Default: masks ITR" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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98 <param name="mask_file"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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99 type="data"
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100 format="csv"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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101 optional="true"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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102 label="Mask additional sites"
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103 help="Run squirrel in alignment with QC to generate the SNP mask file." />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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104 <param name="bg_file"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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105 type="data"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
106 format="fasta"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
107 optional="true"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
108 label="Background file - leave empty for automatic background sequences."
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
109 help="Include a default background set of sequences for the phylogenetics pipeline. The set will be determined by previous 'clade' setting"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
110 <param name="out_group"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
111 type="text"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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112 label="Specify outgroup(s)"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
113 help="Specify which MPXV outgroup(s) in the alignment to use in the phylogeny. These will get pruned out from the final tree."/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
114 <param name="fig_height"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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115 label="Overwrite tree figure default height"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
116 type="integer"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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117 min="0"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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118 value="25"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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119 optional="true">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
120 </param>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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121 <param name="fig_width"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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122 label="Overwrite tree figure default width"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
123 type="integer"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
124 min="0"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
125 value="40"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
126 optional="true">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
127 </param>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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128 </section>
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129 </inputs>
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130
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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131 <outputs>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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132 <!-- standard outputs-->
3
46a0e11a7607 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel commit 68ea06281ba78b828b8d1947745161697dc0fbc5
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133 <data name="tree" format="nexus" label="${tool.name} - phylogenetic tree" />
0
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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134 <data name="alignment" format="fasta" label="${tool.name} - aligned sequences" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
135 <!-- apobec3 outputs-->
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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136 <data name="svg" format="svg" label="${tool.name} - phylotree svg image">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
137 <filter>apobec3</filter>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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138 </data>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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139 <data name="png" format="png" label="${tool.name} - phylotree png image">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
140 <filter>apobec3</filter>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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141 </data>
3
46a0e11a7607 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel commit 68ea06281ba78b828b8d1947745161697dc0fbc5
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142 <data name="aa_recon" format="csv" label="${tool.name} - aa mutations ancestral reconstruction">
0
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
143 <filter>apobec3</filter>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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144 </data>
3
46a0e11a7607 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel commit 68ea06281ba78b828b8d1947745161697dc0fbc5
iuc
parents: 1
diff changeset
145 <data name="branch_snps" format="csv" label="${tool.name} - apobec3 nt mutations">
0
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
146 <filter>apobec3</filter>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
147 </data>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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148 </outputs>
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149
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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150 <tests>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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151 <test expect_num_outputs="2">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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152 <param name="sequences" value="test-sequences.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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153 <param name="bg_file" value="test-background.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
154 <param name="out_group" value="KJ642615" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
155 <param name="apobec3" value="false" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
156 <output name="alignment" file="sequences.aln.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
157 <output name="tree">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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158 <assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
159 <has_line_matching expression="#NEXUS"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
160 </assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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161 </output>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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162 </test>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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163
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
164 <test expect_num_outputs="6">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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165 <param name="sequences" value="test-sequences.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
166 <param name="bg_file" value="test-background.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
167 <param name="out_group" value="KJ642615" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
168 <param name="apobec3" value="true" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
169 <output name="alignment" file="sequences.aln.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
170 <output name="tree">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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171 <assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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172 <has_line_matching expression="#NEXUS"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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173 </assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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174 </output>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
175 <output name="svg">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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176 <assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
177 <has_text text="svg xmlns:"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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178 <has_text text="DQ011155"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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179 </assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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180 </output>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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181 <output name="png" file="sequences.tree.png" ftype="png" compare="sim_size" delta="1000" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
182 <output name="aa_recon" file="sequences.tree.amino_acid.reconstruction.csv" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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183 <output name="branch_snps" file="sequences.tree.branch_snps.reconstruction.csv" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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184 </test>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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185
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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186 </tests>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
187 <help><![CDATA[
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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188 squirrel allows for rapidly producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
189
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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190 Ensure your input sequences are of a singular clade and not mixed CladeI/CladeII. CladeI and CladeIa/b are fine to combine.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
191
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
192 **Alignment**
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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193 Squirrel maps each query genome in the input file against a reference genome specific to each clade using minimap2. Using gofasta, the mapping file is then converted into a multiple sequence alignment.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
194
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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195 For Clade II, the reference used is NC_063383 and for Clade I, we use NC_003310. This means that all coordinates within an alignment will be relative to these references. A benefit of this is that within a clade, alignment files and be combined without having to recalculate the alignment. Note however that insertions relative to the reference sequence will not be included in the alignment.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
196
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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197 Squirrel by default creates a single alignment fasta file. Using the genbank coordinates for NC_063383 it also has the ability to extract the aligned coding sequences either as separate records or as a concatenated alignment. This can facilitate codon-aware phylogenetic or sequence analysis.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
198
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
199 **APOBEC3**
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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200 Enrichment of APOBEC3-mutations in the MPXV population are a signature of sustained human-to-human transmission. Identifying APOBEC3-like mutations in MPXV genomes from samples in a new outbreak can be a piece of evidence to support sustained human transmission of mpox. Squirrel can run an APOBEC3-reconstruction and map these mutations onto the phylogeny.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
201
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
202 **Default Masking**
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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203 Squirrel performs masking (replacement with N) on low-complexity or repetitive regions that have been characterised for Clade I and II. These regions are defined in to_mask.cladeii.csv and to_mask.cladei.csv (see github: https://github.com/aineniamh/squirrel/blob/main/squirrel/data/).
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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204
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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205 **Additional Masking**
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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206 Additional mask file can be provided to mask sites in addition to default masking. To generate additional masking file, run the galaxy tool *squirrel-qc*
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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207
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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208
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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209 ]]></help>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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211 <expand macro="citations" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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212 </tool>