Mercurial > repos > iuc > freyja_demix

annotate macros.xml @ 1:c0a0e79d7196 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
author iuc
date Fri, 07 Jul 2023 05:51:15 +0000
parents fc6252e78d5b
children 53b22b7dff19
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fc6252e78d5b 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"?>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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2 <macros>
1
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
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3 <token name="@TOOL_VERSION@">1.4.4</token>
0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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4 <token name="@VERSION_SUFFIX@">0</token>
fc6252e78d5b 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>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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6 <xml name="biotools">
fc6252e78d5b 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>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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9 </xrefs>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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10 </xml>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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11 <xml name="requirements">
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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12 <requirements>
fc6252e78d5b 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>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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14 <yield/>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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15 </requirements>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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16 </xml>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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17 <xml name="version">
fc6252e78d5b 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>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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19 </xml>
fc6252e78d5b 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[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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21 #if $usher_update_option.choice == 'update'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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22 freyja update &&
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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23 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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24 ]]></token>
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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25 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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26 ln -s '$variants_file' 'variants_file.vcf' &&
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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27 ]]></token>
fc6252e78d5b 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[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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29 #if $variants_file.ext == 'vcf'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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30 'variants_file.vcf'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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31 #else
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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32 '$variants_file'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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33 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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34 '$depth_file'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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35 #if $eps
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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36 --eps '${eps}'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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37 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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38 #if $meta
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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39 --meta '${meta}'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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40 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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41 $confirmedonly
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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42 ]]></token>
fc6252e78d5b 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[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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44 #if $usher_update_option.choice == 'custom'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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45 --barcodes '${usher_update_option.usher_barcodes}'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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46 #end if
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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47 ]]></token>
fc6252e78d5b 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[
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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49 echo '${plot_format.plot_title}' > plot_title.txt &&
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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50 echo '${plot_format.plot_intro}' > plot_intro.txt &&
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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51 freyja dash
1
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
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52 --mincov $plot_format.mincov
0
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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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>
fc6252e78d5b 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
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
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65 $plot_format.lineages
c0a0e79d7196 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
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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
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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72 --output abundances_plot.pdf
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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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>
fc6252e78d5b 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'
fc6252e78d5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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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>