Mercurial > repos > iuc > freyja_variants

annotate macros.xml @ 2:059374388b8f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit dcb5fdc6a89563af33a1783e4f70754d6611585c
author iuc
date Thu, 10 Oct 2024 18:28:40 +0000
parents 1f467ed22412
children
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08c2d81e7942 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"?>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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2 <macros>
2
059374388b8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit dcb5fdc6a89563af33a1783e4f70754d6611585c
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3 <token name="@TOOL_VERSION@">1.5.1</token>
0
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4 <token name="@VERSION_SUFFIX@">0</token>
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5 <token name="@PROFILE@">21.01</token>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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6 <xml name="biotools">
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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7 <xrefs>
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8 <xref type="bio.tools">freyja</xref>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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9 </xrefs>
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10 </xml>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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11 <xml name="requirements">
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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12 <requirements>
08c2d81e7942 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>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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14 <yield/>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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15 </requirements>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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16 </xml>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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17 <xml name="version">
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18 <version_command>freyja --version</version_command>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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19 </xml>
08c2d81e7942 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[
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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21 #if $usher_update_option.choice == 'update'
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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22 freyja update &&
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23 #end if
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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24 ]]></token>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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25 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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26 ln -s '$variants_file' 'variants_file.vcf' &&
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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27 ]]></token>
08c2d81e7942 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[
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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29 #if $variants_file.ext == 'vcf'
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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30 'variants_file.vcf'
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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31 #else
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32 '$variants_file'
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33 #end if
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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34 '$depth_file'
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35 #if $eps
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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36 --eps '${eps}'
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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37 #end if
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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38 #if $meta
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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39 --meta '${meta}'
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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40 #end if
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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41 $confirmedonly
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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42 ]]></token>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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43 <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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44 #if $usher_update_option.choice == 'custom'
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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45 --barcodes '${usher_update_option.usher_barcodes}'
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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46 #end if
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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47 ]]></token>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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48 <token name="@DASH_COMMAND@"><![CDATA[
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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49 echo '${plot_format.plot_title}' > plot_title.txt &&
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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50 echo '${plot_format.plot_intro}' > plot_intro.txt &&
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51 freyja dash
1
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52 --mincov $plot_format.mincov
0
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53 #if $need_aggregation.choice == 'no'
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54 '$tsv_aggregated'
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55 #else
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56 'aggregated.tsv'
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57 #end if
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58 '$plot_format.csv_meta'
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59 plot_title.txt
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60 plot_intro.txt
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61 --output abundances_dashboard.html
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62 ]]></token>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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63 <token name="@PLOT_COMMAND@"><![CDATA[
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64 freyja plot
1
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65 $plot_format.lineages
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66 --mincov $plot_format.mincov
0
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67 #if $need_aggregation.choice == 'no'
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68 '$tsv_aggregated'
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69 #else
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70 'aggregated.tsv'
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71 #end if
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72 --output abundances_plot.pdf
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73 #if $plot_format.csv_meta
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74 --times '${plot_format.csv_meta}'
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75 #end if
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76 #if $plot_format.interval == 'MS'
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77 --interval MS
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78 #else
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79 --interval D
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80 --windowsize 70
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81 #end if
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82 ]]></token>
08c2d81e7942 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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83 <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[
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84 #if $plot_format.choice == 'dash'
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85 @DASH_COMMAND@
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86 #else if $plot_format.choice == 'plot'
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87 freyja plot
1
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88 $plot_format.lineages
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89 --mincov $plot_format.mincov
0
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90 #if $need_aggregation.choice == 'no'
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91 $tsv_aggregated
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92 #else
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93 aggregated.tsv
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94 #end if
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95 --output abundances_plot.pdf
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96 #if $plot_format.need_metadata.choice == 'yes'
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97 --times '${plot_format.need_metadata.csv_meta}'
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98 #if $plot_format.need_metadata.interval == 'MS'
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99 --interval MS
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100 #else
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101 --interval D
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102 --windowsize 70
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103 #end if
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104 #end if
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105 #else if $plot_format.choice == 'plot_and_dash'
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106 @DASH_COMMAND@ &&
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107 @PLOT_COMMAND@
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108 #end if
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109 ]]></token>
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110 <xml name="demixing_common_options">
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111 <param name="depth_file" type="data" format="tabular" label="Sequencing depth file"/>
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112 <conditional name="usher_update_option">
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113 <param name="choice" type="select" label="Source of UShER barcodes data"
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114 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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115 <option value="repo" selected="true">Use data shipped with the tool (can be
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116 outdated)
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117 </option>
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118 <option value="custom">Provide a custom barcodes file</option>
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119 <!--<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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120 </param>
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121 <when value="repo"/>
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122 <when value="custom">
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123 <param name="usher_barcodes" type="data" format="csv" label="UShER barcodes file"/>
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124 </when>
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125 <!--<when value="update" />-->
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126 </conditional>
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127 <param argument="--meta" type="data" format="json" optional="true"
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128 label="Custom lineage metadata file"
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129 help="For additional flexibility and reproducibility of analyses, a custom lineage-to-contellation mapping metadata file can be provided."/>
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130 <param argument="--eps" type="float" optional="true"
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131 label="Minimum lineage abundance tp include"
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132 help="e.g. 0.0001."/>
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133 <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue=""
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134 checked="false"
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135 label="Remove unconfirmed lineages from the analysis"
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136 help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
1
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137 <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue=""
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138 checked="false"
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139 label="Use larger library with non-public lineages"
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140 help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
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141 </xml>
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142 <xml name="plot_lineages">
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143 <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
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144 checked="false" label="Use lineage specific breakdown"/>
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145 </xml>
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146 <xml name="plot_mincov">
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147 <param argument="--mincov" type="float" min="0" max="100" value="60"
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148 label="Minimum genome coverage"
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149 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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150 </xml>
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151 <token name="@HELP_HEADER@"><![CDATA[
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152 What it does
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153 ============
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154
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155 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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156
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157 General information
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158 ===================
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159
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160 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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161
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162 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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163 ]]></token>
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164 <xml name="citations">
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165 <citations>
1
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166 <citation type="doi">10.1038/s41586-022-05049-6</citation>
0
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167 </citations>
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168 </xml>
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169 </macros>