Mercurial > repos > johnlees > poppunk

annotate tools/PopPUNK/poppunk_cluster.xml @ 3:a3613553c65f draft default tip

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planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846-dirty
author johnlees
date Thu, 16 May 2019 15:35:29 -0400
parents 1d7ba8646dd1
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1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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1 <tool id="poppunk_cluster" name="PopPUNK (cluster)" version="1.1.6">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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2 <description>Cluster bacterial genomes</description>
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3
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4 <requirements>
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5 <requirement type="package" version="1.1.6">poppunk</requirement>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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6 </requirements>
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7
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8 <version_command><![CDATA[
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9 poppunk --version
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10 ]]></version_command>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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11
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12 <command detect_errors="exit_code"><![CDATA[
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13 ##Set up input files
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14 ##echo "$input_assemblies" | tr ',' '\n' > r_files.txt
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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15 #for $input in $input_assemblies
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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16 ln -s $input $input.element_identifier && echo $input.element_identifier >> r_files.txt;
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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17 #end for
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18
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19 ## command line 1 (create db)
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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20 echo "
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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21 poppunk
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22 --create-db
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23 --r-files r_files.txt
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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24 --output poppunk_db
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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25 --threads \${GALAXY_SLOTS:-1}
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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26 --min-k $min_k
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27 --max-k $max_k
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28 --k-step $k_step
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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29 --sketch-size $sketch_size
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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30 --max-a-dist $max_a_dist
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31 #if $ignore_length
a3613553c65f planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846-dirty
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32 --ignore-length
2
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33 #end if
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34 --no-stream
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35 " > poppunk_1.sh
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36
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37 && sh poppunk_1.sh
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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38
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39 ## command line 2 (fit model)
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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40 && echo "
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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41 poppunk
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42 --fit-model
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43 --distances poppunk_db/poppunk_db.dists
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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44 --ref-db poppunk_db
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45 --output poppunk_db
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46
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47 ## mode
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48 #if str( $model.model_mode ) == "gmm":
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49 --K ${model.K}
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50 #end if
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51 #if str( $model.model_mode ) == "dbscan":
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52 --dbscan
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53 --D $model.D
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54 --min-cluster-prop $model.min_cluster_prop
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55 #end if
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56
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57 #if not $no_full_db or $refine.refine_model
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58 --full-db
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59 #end if
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60
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61 #if not $refine.refine_model:
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62 #if $external_clusters
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63 --external-clustering $external_clusters
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64 #end if
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65
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66 ## viz
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67 #if $cytoscape:
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68 --cytoscape
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69 #end if
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70 #if $viz.microreact:
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71 --microreact
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72 --rapidnj rapidnj
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73 --perplexity $viz.perplexity
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74 #end if
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75 #if ($cytoscape or $viz.microreact) and $info_csv:
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76 --info-csv $info_csv
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77 #end if
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78 #end if
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79
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80 " > poppunk_2.sh
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81
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82 && sh poppunk_2.sh
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83
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84 ## command line 3 (refine)
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85 #if $refine.refine_model:
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86 && echo "
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87 poppunk
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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parents:
diff changeset
88 --refine-model
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
89 --distances poppunk_db/poppunk_db.dists
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
90 --ref-db poppunk_db
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
91 --output poppunk_db
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
92 --threads \${GALAXY_SLOTS:-1}
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
93 --pos-shift $refine.pos_shift
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
94 --neg-shift $refine.neg_shift
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
95
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
96 #if not $no_full_db
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
97 --full-db
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
98 #end if
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
99
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
100 #if $external_clusters
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
101 --external-clustering $external_clusters
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
102 #end if
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
103
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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104 ## viz
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
105 #if $cytoscape:
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
106 --cytoscape
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
107 #end if
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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108 #if $viz.microreact:
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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109 --microreact
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
110 --rapidnj rapidnj
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
111 --perplexity $viz.perplexity
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
112 #end if
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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113 #if ($cytoscape or $viz.microreact) and $info_csv:
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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114 --info-csv $info_csv
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
115 #end if
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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116
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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117 " > poppunk_3.sh
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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118
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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119 && sh poppunk_3.sh;
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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120 #end if
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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121
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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122 ]]></command>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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123
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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124 <inputs>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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125
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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126 <!-- input files -->
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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127 <param name="input_assemblies" type="data" format="fasta" multiple="true" label="FASTA datasets (assemblies)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
128 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
129
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
130 <!-- model type -->
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
131 <conditional name="model">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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132 <param name="model_mode" type="select" label="Choose a model to use" help="See documentation or description below for advice, if default does not work." display="radio">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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133 <option value="gmm" selected="true">GMM</option>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
134 <option value="dbscan">DBSCAN</option>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
135 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
136 <!-- model options -->
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
137 <when value="gmm">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
138 <param name="K" type="integer" value="3" min="2" max="10" label="Number of mixture components">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
139 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
140 </when>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
141 <when value="dbscan">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
142 <param name="D" type="integer" value="100" min="2" max="500" label="Maximum number of spatial clusters">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
143 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
144 <param name="min_cluster_prop" type="float" value="0.0001" min="0.00001" max="0.1" label="Minimum proportion of points in a cluster">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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diff changeset
145 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
146 </when>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
147 </conditional>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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148
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
149 <!-- refine model options -->
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
150 <conditional name="refine">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
151 <param name="refine_model" type="boolean" checked="false" label="Run model refinement after model fit">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
152 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
153 <when value="true">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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154 <param name="pos_shift" type="float" value="0.2" min="0.0" max="1.0" label="Maximum amount to move the boundary away from origin">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
155 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
156 <param name="neg_shift" type="float" value="0.4" min="0.0" max="1.0" label="Minimum amount to move the boundary away from origin">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
157 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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diff changeset
158 </when>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
159 <when value='false' />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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160 </conditional>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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161
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
162 <!-- further analysis options -->
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
163 <conditional name="viz">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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164 <param name="microreact" type="boolean" checked="true" label="Make visualisations for microreact (recommended)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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165 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
166 <when value="true">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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167 <param name="perplexity" type="float" value="20.0" min="5.0" max="100.0" label="Perplexity parameter for accessory plot t-SNE">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
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168 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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169 </when>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
diff changeset
170 <when value='false' />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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171 </conditional>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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172 <param name="cytoscape" type="boolean" checked="false" label="Make visualisations for cytoscape">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
johnlees
parents:
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173 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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174
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johnlees
parents:
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175 <!-- output options -->
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176 <param name="no_full_db" type="boolean" checked="true" label="Select representative references">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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177 </param>
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178
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179 <param name="external_clusters" type="data" format="csv" optional="true" label="External cluster labels to add (e.g. MLST/serotype)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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180 </param>
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181 <param name="info_csv" type="data" format="csv" optional="true" label="Epidemiological information CSV formatted for microreact">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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182 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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183
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184 <!-- kmer comparison options -->
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185 <param name="min_k" type="integer" value="13" min="7" max="31" label="Minimum k-mer length">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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186 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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187 <param name="max_k" type="integer" value="29" min="7" max="31" label="Maximum k-mer length">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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188 </param>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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189 <param name="k_step" type="integer" value="3" min="2" max="5" label="Step size between k-mer lengths">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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190 </param>
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191 <param name="sketch_size" type="integer" value="10000" min="1000" max="2000000" label="Sketch size">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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192 </param>
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193
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194 <!-- quality control options -->
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195 <param name="max_a_dist" type="float" value="0.5" min="0.0" max="1.0" label="Maximum accessory distance to permit">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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196 </param>
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197 <param name="ignore_length" type="boolean" checked="false" label="Ignore assembly length outliers">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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198 </param>
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199
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200 </inputs>
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201
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202 <outputs>
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203 <data name="clusters" format="csv" from_work_dir="poppunk_db/poppunk_db_clusters.csv" label="${tool.name} on ${on_string} (cluster assignment)" />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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204 <data name="distances" format="png" from_work_dir="poppunk_db/poppunk_db_distanceDistribution.png" label="${tool.name} on ${on_string} (distance plot)" />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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205 <data name="references" format="txt" from_work_dir="poppunk_db/poppunk_db.refs" label="${tool.name} on ${on_string} (selected references)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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206 <filter>no_full_db == True</filter>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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207 </data>
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208 <data name="gmm_plot" format="png" from_work_dir="poppunk_db/poppunk_db_DPGMM_fit.png" label="${tool.name} on ${on_string} (GMM cluster plot)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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209 <filter>model['model_mode'] == 'gmm'</filter>
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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210 </data>
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211 <data name="gmm_contours" format="pdf" from_work_dir="poppunk_db/poppunk_db_DPGMM_fit_contours.pdf" label="${tool.name} on ${on_string} (GMM contour plot)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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212 <filter>model['model_mode'] == 'gmm'</filter>
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213 </data>
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214 <data name="dbscan_plot" format="png" from_work_dir="poppunk_db/poppunk_db_dbscan.png" label="${tool.name} on ${on_string} (DBSCAN cluster plot)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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215 <filter>model['model_mode'] == 'dbscan'</filter>
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216 </data>
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217 <data name="refine_plot" format="png" from_work_dir="poppunk_db/poppunk_db_refined_fit.png" label="${tool.name} on ${on_string} (refine model plot)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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218 <filter>refine['refine_model'] == True</filter>
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219 </data>
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220 <data name="cytoscape_network" format="data" from_work_dir="poppunk_db/poppunk_db_cytoscape.graphml" label="${tool.name} on ${on_string} (cytoscape network)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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221 <filter>cytoscape == True</filter>
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222 </data>
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223 <data name="cytoscape_clusters" format="csv" from_work_dir="poppunk_db/poppunk_db_cytoscape.csv" label="${tool.name} on ${on_string} (cytoscape csv)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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224 <filter>cytoscape == True</filter>
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225 </data>
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226 <data name="microreact_clusters" format="csv" from_work_dir="poppunk_db/poppunk_db_microreact_clusters.csv" label="${tool.name} on ${on_string} (microreact csv)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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227 <filter>viz['microreact'] == True</filter>
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228 </data>
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229 <data name="microreact_tree" format="newick" from_work_dir="poppunk_db/poppunk_db_core_NJ.nwk" label="${tool.name} on ${on_string} (microreact tree)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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230 <filter>viz['microreact'] == True</filter>
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231 </data>
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232 <data name="microreact_dot" format="graph_dot" from_work_dir="poppunk_db/poppunk_db_perplexity${perplexity}_accessory_tsne.dot" label="${tool.name} on ${on_string} (microreact dot)">
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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233 <filter>viz['microreact'] == True</filter>
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234 </data>
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235 </outputs>
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236
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237 <tests>
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238 <test>
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239 <param name='input_assemblies' value='12673_8_24.contigs_velvet.fa,12673_8_34.contigs_velvet.fa,12673_8_43.contigs_velvet.fa,12754_4_71.contigs_velvet.fa,12754_4_77.contigs_velvet.fa' />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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240 <param name='model_mode' value='gmm' />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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241 <param name='K' value='4' />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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242 <param name='microreact' value='false' />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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243 <param name='no_full_db' value='false' />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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244 <output name="clusters" ftype='csv' file="clusters.csv" />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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245 <output name="distances" ftype='png' file="distances.png" />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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246 <output name="references" file="refs.txt" />
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247 <output name="gmm_plot" ftype='png' file="gmm_fit.png" />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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248 <output name="gmm_contours" ftype='pdf' file="gmm_contours.pdf" />
1d7ba8646dd1 planemo upload for repository https://github.com/johnlees/PopPUNK_galaxy/tree/master/PopPUNK commit a543b2e4a4e95808997d2d5423f9232d1c517846
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249 </test>
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250 </tests>
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251
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252 <help><![CDATA[
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253 **What it does**
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254
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255 PopPUNK will calculate core and accessory distance between input assemblies using variable length k-mers. A model will be fitted to all of these distances to determine genetic clusters for all inpits.
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256
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257 ------
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258
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259 **Description**
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260
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261 The most important thing to check is that in the output plot the component (blob) closest to the origin has been correctly identified - this should be checked in the cluster/model plot output. If it has not, you may wish to try another model. Some broad advice:
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262
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263 * DBSCAN is a good default, but may lead to unclassified points (black). If there are a large number of these consider another model.
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264 * GMM will work well with well-separated components and an appropriate choice of K (consider increasing it based on the number of components that can be seen).
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265 * The refine mode should be added in recombining species, which can be seen from the output plots if the coloured components are overlapping, or if there is a blur of points rather than discrete blobs of points..
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266 ]]></help>
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267
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268 <citations>
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269 <citation type='bibtex'>
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270 @article{Lees01022019,
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271 author = {Lees, John A. and Harris, Simon R. and Tonkin-Hill, Gerry and Gladstone, Rebecca A. and Lo, Stephanie W. and Weiser, Jeffrey N. and Corander, Jukka and Bentley, Stephen D. and Croucher, Nicholas J.},
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272 title = {Fast and flexible bacterial genomic epidemiology with PopPUNK},
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273 volume = {29},
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274 number = {2},
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275 pages = {304-316},
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276 year = {2019},
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277 doi = {10.1101/gr.241455.118},
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278 abstract ={The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (Population Partitioning Using Nucleotide K-mers), a software implementing scalable and expandable annotation- and alignment-free methods for population analysis and clustering. Variable-length k-mer comparisons are used to distinguish isolates’ divergence in shared sequence and gene content, which we demonstrate to be accurate over multiple orders of magnitude using data from both simulations and genomic collections representing 10 taxonomically widespread species. Connections between closely related isolates of the same strain are robustly identified, despite interspecies variation in the pairwise distance distributions that reflects species’ diverse evolutionary patterns. PopPUNK can process 103–104 genomes in a single batch, with minimal memory use and runtimes up to 200-fold faster than existing model-based methods. Clusters of strains remain consistent as new batches of genomes are added, which is achieved without needing to reanalyze all genomes de novo. This facilitates real-time surveillance with consistent cluster naming between studies and allows for outbreak detection using hundreds of genomes in minutes. Interactive visualization and online publication is streamlined through the automatic output of results to multiple platforms. PopPUNK has been designed as a flexible platform that addresses important issues with currently used whole-genome clustering and typing methods, and has potential uses across bacterial genetics and public health research.},
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279 URL = {http://genome.cshlp.org/content/29/2/304.abstract},
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280 eprint = {http://genome.cshlp.org/content/29/2/304.full.pdf+html},
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281 journal = {Genome Research}
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282 }</citation>
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283 </citations>
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284 </tool>