Mercurial > repos > iuc > squirrel_phylo

annotate squirrel-phylo.xml @ 0:14936593e454 draft

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planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
author iuc
date Thu, 16 Jan 2025 07:07:17 +0000
parents
children 153c1ee28c48
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0
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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1 <tool id="squirrel_phylo" name="Squirrel Phylo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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2 <description>Phylogenetic and APOBEC3 analysis of MPXV (Mpox virus)</description>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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3 <macros>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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4 <import>macros.xml</import>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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5 </macros>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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6 <expand macro="requirements"/>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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7 <expand macro="version_command"/>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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9 <command detect_errors="exit_code"><![CDATA[
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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10 #set $alignment_output = 'input.aln.fasta'
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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11 #set $tree_output = 'input.tree'
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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12
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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13 #if $apobec3
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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14 #set $aa_recon_output = "input.tree.amino_acid.reconstruction.csv"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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15 #set $branch_snps_output = "input.tree.branch_snps.reconstruction.csv"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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16 #set $svg_output = "input.tree.svg"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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17 #set $png_output = "input.tree.png"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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18 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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19
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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20 ln -s '${sequences}' input.fasta &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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21
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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22 squirrel
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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23 #if $apobec3
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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24 --run-apobec3-phylo
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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25 --fig-height $fig_height
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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26 --fig-width $fig_width
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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27 #else
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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28 --run-phylo
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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29 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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30
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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31 --clade $clade
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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32
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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33 #if $mask_file
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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34 --additional-mask $mask_file
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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35 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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36
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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37 #if $bg_file
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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38 --background-file '$bg_file'
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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39 #else
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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40 --include-background
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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41 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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42
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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43 #if $out_group
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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44 --outgroups $out_group
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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45 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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46
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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47 $no_mask
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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48 $no_iter_mask
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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49
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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50 --threads \${GALAXY_SLOTS:-1}
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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51 input.fasta &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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52
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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53 mv '${alignment_output}' '$alignment' &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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54 mv '${tree_output}' '$tree'
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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55
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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56 #if $apobec3
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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57 && mv '${aa_recon_output}' '$aa_recon' &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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58 mv '${branch_snps_output}' '$branch_snps' &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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59 mv '${svg_output}' '$svg' &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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60 mv '${png_output}' '$png'
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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61 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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62 ]]></command>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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63
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64 <inputs>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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65 <param name="sequences"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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66 type="data"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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67 format="fasta"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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68 label="Sequences in fasta format"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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69 help="You can upload a FASTA sequence to the history and use it as reference" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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70 <param name="apobec3"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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71 type="boolean"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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72 checked="false"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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73 label="Run additional APOBEC3-mutation reconstruction pipeline" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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74 <param name="clade"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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75 type="select"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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76 label="Select MPXV Clade">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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77 <option value="cladei">Clade I</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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78 <option value="cladeia">Clade Ia</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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79 <option value="cladeib">Clade Ib</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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80 <option value="cladeii">Clade II</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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81 <option value="cladeiia">Clade IIa</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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82 <option value="cladeiib">Clade IIb</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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83 </param>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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84 <section name="other_settings" expanded="false" title="Additional Settings">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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85 <param name="no_mask"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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86 type="boolean"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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87 truevalue="--no-mask"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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88 falsevalue=""
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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89 label="SKIP masking repeat regions?"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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90 help="Set to True to Skip masking of repetitive regions. Default: masks repeat regions." />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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91 <param name="no_iter_mask"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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92 type="boolean"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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93 truevalue="--no-itr-mask"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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94 falsevalue=""
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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95 label="SKIP masking of end ITR?"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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96 help="Set to True to skip masking of end ITR. Default: masks ITR" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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97 <param name="mask_file"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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98 type="data"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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99 format="csv"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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100 optional="true"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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101 label="Mask additional sites"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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102 help="Run squirrel in alignment with QC to generate the SNP mask file." />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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103 <param name="bg_file"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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104 type="data"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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105 format="fasta"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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106 optional="true"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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107 label="Background file - leave empty for automatic background sequences."
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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108 help="Include a default background set of sequences for the phylogenetics pipeline. The set will be determined by previous 'clade' setting"/>
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109 <param name="out_group"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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110 type="text"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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111 label="Specify outgroup(s)"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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112 help="Specify which MPXV outgroup(s) in the alignment to use in the phylogeny. These will get pruned out from the final tree."/>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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113 <param name="fig_height"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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114 label="Overwrite tree figure default height"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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115 type="integer"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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116 min="0"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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117 value="25"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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118 optional="true">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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119 </param>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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120 <param name="fig_width"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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121 label="Overwrite tree figure default width"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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122 type="integer"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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123 min="0"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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124 value="40"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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125 optional="true">
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126 </param>
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127 </section>
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128 </inputs>
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129
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130 <outputs>
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131 <!-- standard outputs-->
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132 <data name="tree" format="newick" label="${tool.name} - phylogenetic tree" />
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133 <data name="alignment" format="fasta" label="${tool.name} - aligned sequences" />
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134 <!-- apobec3 outputs-->
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135 <data name="svg" format="svg" label="${tool.name} - phylotree svg image">
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136 <filter>apobec3</filter>
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137 </data>
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138 <data name="png" format="png" label="${tool.name} - phylotree png image">
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139 <filter>apobec3</filter>
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140 </data>
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141 <data name="aa_recon" format="png" label="${tool.name} - aa mutations ancestral reconstruction">
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142 <filter>apobec3</filter>
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143 </data>
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144 <data name="branch_snps" format="png" label="${tool.name} - apobec3 nt mutations">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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145 <filter>apobec3</filter>
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146 </data>
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147 </outputs>
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148
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149 <tests>
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150 <test expect_num_outputs="2">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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151 <param name="sequences" value="test-sequences.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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152 <param name="bg_file" value="test-background.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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153 <param name="out_group" value="KJ642615" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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154 <param name="apobec3" value="false" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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155 <output name="alignment" file="sequences.aln.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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156 <output name="tree">
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157 <assert_contents>
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158 <has_line_matching expression="#NEXUS"/>
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159 </assert_contents>
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160 </output>
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161 </test>
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162
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163 <test expect_num_outputs="6">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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164 <param name="sequences" value="test-sequences.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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165 <param name="bg_file" value="test-background.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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166 <param name="out_group" value="KJ642615" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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167 <param name="apobec3" value="true" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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168 <output name="alignment" file="sequences.aln.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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169 <output name="tree">
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170 <assert_contents>
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171 <has_line_matching expression="#NEXUS"/>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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172 </assert_contents>
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173 </output>
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174 <output name="svg">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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175 <assert_contents>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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176 <has_text text="svg xmlns:"/>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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177 <has_text text="DQ011155"/>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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178 </assert_contents>
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179 </output>
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180 <output name="png" file="sequences.tree.png" ftype="png" compare="sim_size" delta="1000" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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181 <output name="aa_recon" file="sequences.tree.amino_acid.reconstruction.csv" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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182 <output name="branch_snps" file="sequences.tree.branch_snps.reconstruction.csv" />
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183 </test>
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184
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185 </tests>
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186 <help><![CDATA[
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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187 squirrel allows for rapidly producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation.
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188
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189 Ensure your input sequences are of a singular clade and not mixed CladeI/CladeII. CladeI and CladeIa/b are fine to combine.
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190
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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191 **Alignment**
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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192 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.
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193
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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194 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.
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195
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196 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.
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197
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198 **APOBEC3**
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199 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.
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200
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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201 **Default Masking**
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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202 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/).
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203
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204 **Additional Masking**
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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205 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*
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206
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207
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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208 ]]></help>
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209
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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210 <expand macro="citations" />
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211 </tool>