Mercurial > repos > iuc > freyja_variants

annotate macros.xml @ 5:d3d7bed79d25 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit f3e2c32cdc7702d165826e89c6a29202fe28182b
author iuc
date Sun, 05 Oct 2025 19:51:29 +0000
parents bc4646c69e90
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
78c93485013d 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"?>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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2 <macros>
5
d3d7bed79d25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit f3e2c32cdc7702d165826e89c6a29202fe28182b
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3 <token name="@TOOL_VERSION@">2.0.1</token>
d3d7bed79d25 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit f3e2c32cdc7702d165826e89c6a29202fe28182b
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4 <token name="@VERSION_SUFFIX@">0</token>
0
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5 <token name="@PROFILE@">21.01</token>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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6 <xml name="biotools">
78c93485013d 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>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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9 </xrefs>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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10 </xml>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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11 <xml name="requirements">
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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12 <requirements>
78c93485013d 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>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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14 <yield/>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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15 </requirements>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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16 </xml>
78c93485013d 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>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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19 </xml>
78c93485013d 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[
78c93485013d 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'
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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22 freyja update &&
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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23 #end if
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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24 ]]></token>
4
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25 <token name="@CUSTOM_BARCODES_LINKING@"><![CDATA[
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26 #if $usher_update_option.choice == 'custom'
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27 ln -s '${usher_update_option.usher_barcodes}' usher_barcodes.csv &&
bc4646c69e90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06
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28 #end if
bc4646c69e90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06
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29 ]]></token>
bc4646c69e90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06
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30 <token name="@CUSTOM_BARCODES_COMMAND@"><![CDATA[
bc4646c69e90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06
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31 #if $usher_update_option.choice == 'custom'
bc4646c69e90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06
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32 --barcodes usher_barcodes.csv
bc4646c69e90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06
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33 #end if
bc4646c69e90 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit cb599a5ca4a1612c5fc8050d6042d52c729a7c06
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34 ]]></token>
0
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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35 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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36 ln -s '$variants_file' 'variants_file.vcf' &&
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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37 ]]></token>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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38 <token name="@STANDARD_INPUT_FOR_BOOT@"><![CDATA[
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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39 #if $variants_file.ext == 'vcf'
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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40 'variants_file.vcf'
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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41 #else
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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42 '$variants_file'
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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43 #end if
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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44 '$depth_file'
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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45 #if $eps
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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46 --eps '${eps}'
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47 #end if
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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48 #if $meta
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49 --meta '${meta}'
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50 #end if
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51 $confirmedonly
3
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52 --pathogen '$pathogen'
0
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53 ]]></token>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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54 <token name="@DASH_COMMAND@"><![CDATA[
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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55 echo '${plot_format.plot_title}' > plot_title.txt &&
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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56 echo '${plot_format.plot_intro}' > plot_intro.txt &&
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57 freyja dash
1
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58 --mincov $plot_format.mincov
0
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59 #if $need_aggregation.choice == 'no'
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60 '$tsv_aggregated'
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61 #else
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62 'aggregated.tsv'
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63 #end if
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64 '$plot_format.csv_meta'
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65 plot_title.txt
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66 plot_intro.txt
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67 --output abundances_dashboard.html
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68 ]]></token>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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69 <token name="@PLOT_COMMAND@"><![CDATA[
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70 freyja plot
1
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71 $plot_format.lineages
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72 --mincov $plot_format.mincov
0
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73 #if $need_aggregation.choice == 'no'
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74 '$tsv_aggregated'
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75 #else
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76 'aggregated.tsv'
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77 #end if
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78 --output abundances_plot.pdf
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79 #if $plot_format.csv_meta
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80 --times '${plot_format.csv_meta}'
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81 #end if
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82 #if $plot_format.interval == 'MS'
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83 --interval MS
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84 #else
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85 --interval D
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86 --windowsize 70
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87 #end if
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88 ]]></token>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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89 <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[
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90 #if $plot_format.choice == 'dash'
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91 @DASH_COMMAND@
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92 #else if $plot_format.choice == 'plot'
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93 freyja plot
1
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94 $plot_format.lineages
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95 --mincov $plot_format.mincov
0
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96 #if $need_aggregation.choice == 'no'
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97 $tsv_aggregated
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98 #else
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99 aggregated.tsv
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100 #end if
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101 --output abundances_plot.pdf
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102 #if $plot_format.need_metadata.choice == 'yes'
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103 --times '${plot_format.need_metadata.csv_meta}'
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104 #if $plot_format.need_metadata.interval == 'MS'
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105 --interval MS
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106 #else
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107 --interval D
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108 --windowsize 70
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109 #end if
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110 #end if
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111 #else if $plot_format.choice == 'plot_and_dash'
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112 @DASH_COMMAND@ &&
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113 @PLOT_COMMAND@
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114 #end if
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115 ]]></token>
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116 <xml name="demixing_common_options">
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117 <param name="depth_file" type="data" format="tabular" label="Sequencing depth file"/>
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118 <conditional name="usher_update_option">
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119 <param name="choice" type="select" label="Source of UShER barcodes data"
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120 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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121 <option value="repo" selected="true">Use data shipped with the tool (can be
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122 outdated)
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123 </option>
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124 <option value="custom">Provide a custom barcodes file</option>
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125 <!--<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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126 </param>
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127 <when value="repo"/>
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128 <when value="custom">
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129 <param name="usher_barcodes" type="data" format="csv" label="UShER barcodes file"/>
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130 </when>
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131 <!--<when value="update" />-->
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132 </conditional>
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133 <param argument="--meta" type="data" format="json" optional="true"
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134 label="Custom lineage metadata file"
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135 help="For additional flexibility and reproducibility of analyses, a custom lineage-to-contellation mapping metadata file can be provided."/>
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136 <param argument="--eps" type="float" optional="true"
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137 label="Minimum lineage abundance tp include"
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138 help="e.g. 0.0001."/>
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139 <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue=""
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140 checked="false"
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141 label="Remove unconfirmed lineages from the analysis"
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142 help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
1
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143 <param argument="--wgisaid" type="boolean" truevalue="--wgisaid" falsevalue=""
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144 checked="false"
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145 label="Use larger library with non-public lineages"
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146 help="Allows to use larger UShER barcodes library extended with GISAID non-public lineages"/>
3
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147 <param argument="--pathogen" type="select" label="Pathogen of interest">
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148 <option value="SARS-CoV-2" selected="true">SARS-CoV-2</option>
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149 <option value="MPXV" selected="true">MPXV</option>
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150 <option value="H5NX" selected="true">H5NX</option>
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151 <option value="H1N1pdm" selected="true">H1N1pdm</option>
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152 <option value="FLU-B-VIC" selected="true">FLU-B-VIC</option>
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153 <option value="MEASLESN450" selected="true">MEASLESN450</option>
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154 <option value="MEASLES" selected="true">MEASLES</option>
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155 <option value="RSVa" selected="true">RSVa</option>
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156 <option value="RSVb" selected="true">RSVb</option>
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157 </param>
1
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158 </xml>
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159 <xml name="plot_lineages">
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160 <param argument="--lineages" type="boolean" truevalue="--lineages" falsevalue=""
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161 checked="false" label="Use lineage specific breakdown"/>
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162 </xml>
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163 <xml name="plot_mincov">
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164 <param argument="--mincov" type="float" min="0" max="100" value="60"
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165 label="Minimum genome coverage"
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166 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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167 </xml>
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168 <token name="@HELP_HEADER@"><![CDATA[
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169 What it does
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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).
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173
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174 General information
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175 ===================
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176
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177 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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178
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179 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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180 ]]></token>
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181 <xml name="citations">
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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182 <citations>
1
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183 <citation type="doi">10.1038/s41586-022-05049-6</citation>
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184 </citations>
78c93485013d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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185 </xml>
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186 </macros>