Mercurial > repos > iuc > squirrel_phylo

annotate squirrel-phylo.xml @ 3:cb39e40802ef 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 13:32:25 +0000
parents 153c1ee28c48
children
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14936593e454 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">
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>
1
153c1ee28c48 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
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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7 <expand macro="requirements"/>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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8 <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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10 <command detect_errors="exit_code"><![CDATA[
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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11 #set $alignment_output = 'input.aln.fasta'
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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12 #set $tree_output = 'input.tree'
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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14 #if $apobec3
14936593e454 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"
14936593e454 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"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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17 #set $svg_output = "input.tree.svg"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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18 #set $png_output = "input.tree.png"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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19 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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21 ln -s '${sequences}' input.fasta &&
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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23 squirrel
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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24 #if $apobec3
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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25 --run-apobec3-phylo
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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26 --fig-height $fig_height
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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27 --fig-width $fig_width
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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28 #else
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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29 --run-phylo
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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30 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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31
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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32 --clade $clade
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14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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34 #if $mask_file
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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35 --additional-mask $mask_file
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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36 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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37
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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38 #if $bg_file
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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39 --background-file '$bg_file'
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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40 #else
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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41 --include-background
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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42 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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43
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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44 #if $out_group
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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45 --outgroups $out_group
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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46 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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47
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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48 $no_mask
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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49 $no_iter_mask
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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51 --threads \${GALAXY_SLOTS:-1}
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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52 input.fasta &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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53
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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54 mv '${alignment_output}' '$alignment' &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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55 mv '${tree_output}' '$tree'
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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56
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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57 #if $apobec3
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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58 && mv '${aa_recon_output}' '$aa_recon' &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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59 mv '${branch_snps_output}' '$branch_snps' &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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60 mv '${svg_output}' '$svg' &&
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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61 mv '${png_output}' '$png'
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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62 #end if
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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63 ]]></command>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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64
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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65 <inputs>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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66 <param name="sequences"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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67 type="data"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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68 format="fasta"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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69 label="Sequences in fasta format"
14936593e454 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" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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71 <param name="apobec3"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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72 type="boolean"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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73 checked="false"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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74 label="Run additional APOBEC3-mutation reconstruction pipeline" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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75 <param name="clade"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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76 type="select"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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77 label="Select MPXV Clade">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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78 <option value="cladei">Clade I</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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79 <option value="cladeia">Clade Ia</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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80 <option value="cladeib">Clade Ib</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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81 <option value="cladeii">Clade II</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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82 <option value="cladeiia">Clade IIa</option>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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83 <option value="cladeiib">Clade IIb</option>
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84 </param>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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85 <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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86 <param name="no_mask"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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87 type="boolean"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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88 truevalue="--no-mask"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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89 falsevalue=""
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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90 label="SKIP masking repeat regions?"
14936593e454 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." />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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92 <param name="no_iter_mask"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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93 type="boolean"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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94 truevalue="--no-itr-mask"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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95 falsevalue=""
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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96 label="SKIP masking of end ITR?"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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97 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
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98 <param name="mask_file"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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99 type="data"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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100 format="csv"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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101 optional="true"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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102 label="Mask additional sites"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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103 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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104 <param name="bg_file"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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105 type="data"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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106 format="fasta"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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107 optional="true"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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108 label="Background file - leave empty for automatic background sequences."
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109 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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110 <param name="out_group"
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111 type="text"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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112 label="Specify outgroup(s)"
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113 help="Specify which MPXV outgroup(s) in the alignment to use in the phylogeny. These will get pruned out from the final tree."/>
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114 <param name="fig_height"
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115 label="Overwrite tree figure default height"
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116 type="integer"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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117 min="0"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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118 value="25"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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119 optional="true">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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120 </param>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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121 <param name="fig_width"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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122 label="Overwrite tree figure default width"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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123 type="integer"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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124 min="0"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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125 value="40"
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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126 optional="true">
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127 </param>
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128 </section>
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129 </inputs>
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130
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131 <outputs>
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132 <!-- standard outputs-->
3
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133 <data name="tree" format="nexus" label="${tool.name} - phylogenetic tree" />
0
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134 <data name="alignment" format="fasta" label="${tool.name} - aligned sequences" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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135 <!-- apobec3 outputs-->
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136 <data name="svg" format="svg" label="${tool.name} - phylotree svg image">
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137 <filter>apobec3</filter>
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138 </data>
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139 <data name="png" format="png" label="${tool.name} - phylotree png image">
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140 <filter>apobec3</filter>
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141 </data>
3
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142 <data name="aa_recon" format="csv" label="${tool.name} - aa mutations ancestral reconstruction">
0
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diff changeset
143 <filter>apobec3</filter>
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144 </data>
3
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145 <data name="branch_snps" format="csv" label="${tool.name} - apobec3 nt mutations">
0
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diff changeset
146 <filter>apobec3</filter>
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147 </data>
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148 </outputs>
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149
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150 <tests>
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151 <test expect_num_outputs="2">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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152 <param name="sequences" value="test-sequences.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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153 <param name="bg_file" value="test-background.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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154 <param name="out_group" value="KJ642615" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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155 <param name="apobec3" value="false" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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156 <output name="alignment" file="sequences.aln.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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157 <output name="tree">
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158 <assert_contents>
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159 <has_line_matching expression="#NEXUS"/>
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160 </assert_contents>
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161 </output>
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162 </test>
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163
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164 <test expect_num_outputs="6">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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165 <param name="sequences" value="test-sequences.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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166 <param name="bg_file" value="test-background.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
167 <param name="out_group" value="KJ642615" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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168 <param name="apobec3" value="true" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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169 <output name="alignment" file="sequences.aln.fasta" />
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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170 <output name="tree">
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171 <assert_contents>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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172 <has_line_matching expression="#NEXUS"/>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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173 </assert_contents>
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174 </output>
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175 <output name="svg">
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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176 <assert_contents>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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177 <has_text text="svg xmlns:"/>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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178 <has_text text="DQ011155"/>
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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179 </assert_contents>
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180 </output>
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181 <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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182 <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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183 <output name="branch_snps" file="sequences.tree.branch_snps.reconstruction.csv" />
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184 </test>
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185
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186 </tests>
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187 <help><![CDATA[
14936593e454 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.
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189
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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.
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191
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192 **Alignment**
14936593e454 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.
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194
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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.
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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196
14936593e454 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.
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198
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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199 **APOBEC3**
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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.
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201
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
202 **Default Masking**
14936593e454 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/).
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204
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205 **Additional Masking**
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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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*
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207
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208
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209 ]]></help>
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210
14936593e454 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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211 <expand macro="citations" />
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212 </tool>