Mercurial > repos > iuc > squirrel_phylo

annotate squirrel-phylo.xml @ 0:b64098b87ea0 draft

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planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
author iuc
date Thu, 16 Jan 2025 07:07:37 +0000
parents
children eaa0b1e114eb
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b64098b87ea0 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">
b64098b87ea0 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>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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3 <macros>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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4 <import>macros.xml</import>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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5 </macros>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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6 <expand macro="requirements"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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7 <expand macro="version_command"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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8
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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9 <command detect_errors="exit_code"><![CDATA[
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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10 #set $alignment_output = 'input.aln.fasta'
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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11 #set $tree_output = 'input.tree'
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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12
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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13 #if $apobec3
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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14 #set $aa_recon_output = "input.tree.amino_acid.reconstruction.csv"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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15 #set $branch_snps_output = "input.tree.branch_snps.reconstruction.csv"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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16 #set $svg_output = "input.tree.svg"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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17 #set $png_output = "input.tree.png"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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18 #end if
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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19
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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20 ln -s '${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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22 squirrel
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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23 #if $apobec3
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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24 --run-apobec3-phylo
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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25 --fig-height $fig_height
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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26 --fig-width $fig_width
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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27 #else
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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28 --run-phylo
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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29 #end if
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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30
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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31 --clade $clade
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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32
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33 #if $mask_file
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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34 --additional-mask $mask_file
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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35 #end if
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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36
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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37 #if $bg_file
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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38 --background-file '$bg_file'
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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39 #else
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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40 --include-background
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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41 #end if
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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42
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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43 #if $out_group
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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44 --outgroups $out_group
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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45 #end if
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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46
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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47 $no_mask
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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48 $no_iter_mask
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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49
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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50 --threads \${GALAXY_SLOTS:-1}
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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51 input.fasta &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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52
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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53 mv '${alignment_output}' '$alignment' &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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54 mv '${tree_output}' '$tree'
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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55
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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56 #if $apobec3
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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57 && mv '${aa_recon_output}' '$aa_recon' &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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58 mv '${branch_snps_output}' '$branch_snps' &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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59 mv '${svg_output}' '$svg' &&
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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60 mv '${png_output}' '$png'
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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61 #end if
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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62 ]]></command>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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63
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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64 <inputs>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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65 <param name="sequences"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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66 type="data"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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67 format="fasta"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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68 label="Sequences in fasta format"
b64098b87ea0 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" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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70 <param name="apobec3"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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71 type="boolean"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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72 checked="false"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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73 label="Run additional APOBEC3-mutation reconstruction pipeline" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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74 <param name="clade"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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75 type="select"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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76 label="Select MPXV Clade">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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77 <option value="cladei">Clade I</option>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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78 <option value="cladeia">Clade Ia</option>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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79 <option value="cladeib">Clade Ib</option>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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80 <option value="cladeii">Clade II</option>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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81 <option value="cladeiia">Clade IIa</option>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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82 <option value="cladeiib">Clade IIb</option>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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83 </param>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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84 <section name="other_settings" expanded="false" title="Additional Settings">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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85 <param name="no_mask"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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86 type="boolean"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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87 truevalue="--no-mask"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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88 falsevalue=""
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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89 label="SKIP masking repeat regions?"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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90 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
iuc
parents:
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91 <param name="no_iter_mask"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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92 type="boolean"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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93 truevalue="--no-itr-mask"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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94 falsevalue=""
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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95 label="SKIP masking of end ITR?"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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96 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
parents:
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97 <param name="mask_file"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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98 type="data"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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99 format="csv"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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100 optional="true"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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101 label="Mask additional sites"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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102 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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103 <param name="bg_file"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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104 type="data"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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105 format="fasta"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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106 optional="true"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
107 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
108 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
109 <param name="out_group"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
110 type="text"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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111 label="Specify outgroup(s)"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
112 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
113 <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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114 label="Overwrite tree figure default height"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
115 type="integer"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
116 min="0"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
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117 value="25"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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118 optional="true">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
119 </param>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
120 <param name="fig_width"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
121 label="Overwrite tree figure default width"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
122 type="integer"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
123 min="0"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
124 value="40"
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
125 optional="true">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
126 </param>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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127 </section>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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128 </inputs>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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129
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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130 <outputs>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
131 <!-- standard outputs-->
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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132 <data name="tree" format="newick" label="${tool.name} - phylogenetic tree" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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133 <data name="alignment" format="fasta" label="${tool.name} - aligned sequences" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
134 <!-- apobec3 outputs-->
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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135 <data name="svg" format="svg" label="${tool.name} - phylotree svg image">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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136 <filter>apobec3</filter>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
137 </data>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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138 <data name="png" format="png" label="${tool.name} - phylotree png image">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
139 <filter>apobec3</filter>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
140 </data>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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141 <data name="aa_recon" format="png" label="${tool.name} - aa mutations ancestral reconstruction">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
142 <filter>apobec3</filter>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
143 </data>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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144 <data name="branch_snps" format="png" label="${tool.name} - apobec3 nt mutations">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
145 <filter>apobec3</filter>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
146 </data>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
147 </outputs>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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148
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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149 <tests>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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150 <test expect_num_outputs="2">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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151 <param name="sequences" value="test-sequences.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
152 <param name="bg_file" value="test-background.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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153 <param name="out_group" value="KJ642615" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
154 <param name="apobec3" value="false" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
155 <output name="alignment" file="sequences.aln.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
156 <output name="tree">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
157 <assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
158 <has_line_matching expression="#NEXUS"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
159 </assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
160 </output>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
161 </test>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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162
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
163 <test expect_num_outputs="6">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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164 <param name="sequences" value="test-sequences.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
165 <param name="bg_file" value="test-background.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
166 <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
167 <param name="apobec3" value="true" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
168 <output name="alignment" file="sequences.aln.fasta" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
diff changeset
169 <output name="tree">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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170 <assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
171 <has_line_matching expression="#NEXUS"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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172 </assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
173 </output>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
174 <output name="svg">
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
175 <assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
176 <has_text text="svg xmlns:"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
177 <has_text text="DQ011155"/>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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178 </assert_contents>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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179 </output>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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180 <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
181 <output name="aa_recon" file="sequences.tree.amino_acid.reconstruction.csv" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
182 <output name="branch_snps" file="sequences.tree.branch_snps.reconstruction.csv" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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183 </test>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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184
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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parents:
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185 </tests>
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
186 <help><![CDATA[
b64098b87ea0 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.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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188
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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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.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
190
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
191 **Alignment**
b64098b87ea0 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.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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193
b64098b87ea0 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.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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195
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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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.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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diff changeset
197
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
198 **APOBEC3**
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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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.
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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200
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
parents:
diff changeset
201 **Default Masking**
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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diff changeset
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/).
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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203
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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204 **Additional Masking**
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
iuc
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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*
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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206
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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207
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208 ]]></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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210 <expand macro="citations" />
b64098b87ea0 planemo upload for repository https://github.com/aineniamh/squirrel commit ed19e40212d1e6651efb3a032d1170f4fd03b989
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211 </tool>