Mercurial > repos > iuc > freyja_aggregate_plot

annotate macros.xml @ 3:e907ef2fc720 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
author iuc
date Fri, 15 Nov 2024 16:43:24 +0000
parents a096c2405955
children d1aa1498fa32
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0
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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1 <?xml version="1.0"?>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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2 <macros>
3
e907ef2fc720 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
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3 <token name="@TOOL_VERSION@">1.5.2</token>
0
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4 <token name="@VERSION_SUFFIX@">0</token>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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5 <token name="@PROFILE@">21.01</token>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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6 <xml name="biotools">
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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7 <xrefs>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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8 <xref type="bio.tools">freyja</xref>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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9 </xrefs>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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10 </xml>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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11 <xml name="requirements">
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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12 <requirements>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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13 <requirement type="package" version="@TOOL_VERSION@">freyja</requirement>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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14 <yield/>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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15 </requirements>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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16 </xml>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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17 <xml name="version">
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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18 <version_command>freyja --version</version_command>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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19 </xml>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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20 <token name="@RUN_FREYJA_UPDATE_COMMAND@"><![CDATA[
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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21 #if $usher_update_option.choice == 'update'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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22 freyja update &&
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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23 #end if
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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24 ]]></token>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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25 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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26 ln -s '$variants_file' 'variants_file.vcf' &&
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
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27 ]]></token>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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28 <token name="@STANDARD_INPUT_FOR_BOOT@"><![CDATA[
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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29 #if $variants_file.ext == 'vcf'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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30 'variants_file.vcf'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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31 #else
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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32 '$variants_file'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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33 #end if
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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34 '$depth_file'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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35 #if $eps
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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36 --eps '${eps}'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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37 #end if
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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38 #if $meta
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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39 --meta '${meta}'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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40 #end if
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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41 $confirmedonly
3
e907ef2fc720 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
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42 --pathogen '$pathogen'
0
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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43 ]]></token>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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44 <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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45 #if $usher_update_option.choice == 'custom'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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46 --barcodes '${usher_update_option.usher_barcodes}'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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47 #end if
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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48 ]]></token>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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49 <token name="@DASH_COMMAND@"><![CDATA[
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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50 echo '${plot_format.plot_title}' > plot_title.txt &&
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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51 echo '${plot_format.plot_intro}' > plot_intro.txt &&
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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52 freyja dash
1
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53 --mincov $plot_format.mincov
0
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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54 #if $need_aggregation.choice == 'no'
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55 '$tsv_aggregated'
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56 #else
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57 'aggregated.tsv'
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58 #end if
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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59 '$plot_format.csv_meta'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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60 plot_title.txt
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61 plot_intro.txt
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62 --output abundances_dashboard.html
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63 ]]></token>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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64 <token name="@PLOT_COMMAND@"><![CDATA[
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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65 freyja plot
1
111d77feb409 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
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66 $plot_format.lineages
111d77feb409 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
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67 --mincov $plot_format.mincov
0
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68 #if $need_aggregation.choice == 'no'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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69 '$tsv_aggregated'
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70 #else
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71 'aggregated.tsv'
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72 #end if
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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73 --output abundances_plot.pdf
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74 #if $plot_format.csv_meta
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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75 --times '${plot_format.csv_meta}'
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76 #end if
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77 #if $plot_format.interval == 'MS'
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78 --interval MS
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79 #else
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80 --interval D
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81 --windowsize 70
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82 #end if
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83 ]]></token>
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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84 <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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85 #if $plot_format.choice == 'dash'
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86 @DASH_COMMAND@
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87 #else if $plot_format.choice == 'plot'
7b000f299096 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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88 freyja plot
1
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89 $plot_format.lineages
111d77feb409 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
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90 --mincov $plot_format.mincov
0
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91 #if $need_aggregation.choice == 'no'
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92 $tsv_aggregated
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93 #else
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94 aggregated.tsv
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95 #end if
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96 --output abundances_plot.pdf
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97 #if $plot_format.need_metadata.choice == 'yes'
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98 --times '${plot_format.need_metadata.csv_meta}'
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99 #if $plot_format.need_metadata.interval == 'MS'
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100 --interval MS
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101 #else
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102 --interval D
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103 --windowsize 70
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104 #end if
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105 #end if
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106 #else if $plot_format.choice == 'plot_and_dash'
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107 @DASH_COMMAND@ &&
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108 @PLOT_COMMAND@
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109 #end if
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110 ]]></token>
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111 <xml name="demixing_common_options">
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112 <param name="depth_file" type="data" format="tabular" label="Sequencing depth file"/>
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113 <conditional name="usher_update_option">
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114 <param name="choice" type="select" label="Source of UShER barcodes data"
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115 help="Freyja ships with an usher_barcodes.csv file, which the tool can access internally. Since this file gets updated rather frequently, you can also download the latest version of the file from https://github.com/andersen-lab/Freyja/raw/main/freyja/data/usher_barcodes.csv, set the dataset's datatype to csv and use it as a custom barcodes file.">
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116 <option value="repo" selected="true">Use data shipped with the tool (can be
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117 outdated)
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118 </option>
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119 <option value="custom">Provide a custom barcodes file</option>
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120 <!--<option value="update">Get updated versions of the curated lineage file as well as the UShER global phylogenetic tree (can cause tool to run slowly)</option>-->
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121 </param>
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122 <when value="repo"/>
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123 <when value="custom">
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124 <param name="usher_barcodes" type="data" format="csv" label="UShER barcodes file"/>
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125 </when>
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126 <!--<when value="update" />-->
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127 </conditional>
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128 <param argument="--meta" type="data" format="json" optional="true"
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129 label="Custom lineage metadata file"
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130 help="For additional flexibility and reproducibility of analyses, a custom lineage-to-contellation mapping metadata file can be provided."/>
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131 <param argument="--eps" type="float" optional="true"
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132 label="Minimum lineage abundance tp include"
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133 help="e.g. 0.0001."/>
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134 <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue=""
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135 checked="false"
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136 label="Remove unconfirmed lineages from the analysis"
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137 help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
1
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138 <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue=""
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139 checked="false"
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140 label="Use larger library with non-public lineages"
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141 help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
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142 <param argument="--pathogen" type="select" label="Pathogen of interest">
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143 <option value="SARS-CoV-2" selected="true">SARS-CoV-2</option>
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144 <option value="MPXV" selected="true">MPXV</option>
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145 <option value="H5NX" selected="true">H5NX</option>
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146 <option value="H1N1pdm" selected="true">H1N1pdm</option>
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147 <option value="FLU-B-VIC" selected="true">FLU-B-VIC</option>
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148 <option value="MEASLESN450" selected="true">MEASLESN450</option>
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149 <option value="MEASLES" selected="true">MEASLES</option>
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150 <option value="RSVa" selected="true">RSVa</option>
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151 <option value="RSVb" selected="true">RSVb</option>
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152 </param>
1
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153 </xml>
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154 <xml name="plot_lineages">
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155 <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
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156 checked="false" label="Use lineage specific breakdown"/>
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157 </xml>
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158 <xml name="plot_mincov">
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159 <param argument="--mincov" type="float" min="0" max="100" value="60"
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160 label="Minimum genome coverage"
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161 help="Include in the plot only samples where the 'coverage' value is greater than the specified --mincov parameter. It excludes samples with coverage values below the minimum coverage threshold. By default, the minimum genome coverage is set at 60 percent."/>
0
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162 </xml>
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163 <token name="@HELP_HEADER@"><![CDATA[
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164 What it does
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165 ============
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166
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167 Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference).
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168
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169 General information
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170 ===================
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171
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172 Freyja is a tool to recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset (BAM aligned to the Hu-1 reference). The method uses lineage-determining mutational "barcodes" derived from the UShER global phylogenetic tree as a basis set to solve the constrained (unit sum, non-negative) de-mixing problem.
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173
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174 Freyja is intended as a post-processing step after primer trimming and variant calling in iVar (Grubaugh and Gangavaparu et al., 2019). From measurements of SNV freqency and sequencing depth at each position in the genome, Freyja returns an estimate of the true lineage abundances in the sample.
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175 ]]></token>
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176 <xml name="citations">
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177 <citations>
1
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178 <citation type="doi">10.1038/s41586-022-05049-6</citation>
0
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179 </citations>
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180 </xml>
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181 </macros>