Mercurial > repos > iuc > freyja_demix

annotate macros.xml @ 0:d4a1c2f9e843 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
author iuc
date Thu, 28 Jul 2022 09:23:22 +0000
parents
children e638a133d318
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0
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
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diff changeset
1 <?xml version="1.0"?>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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2 <macros>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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3 <token name="@TOOL_VERSION@">1.3.8</token>
d4a1c2f9e843 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>
d4a1c2f9e843 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>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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6 <xml name="biotools">
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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7 <xrefs>
d4a1c2f9e843 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>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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9 </xrefs>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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10 </xml>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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11 <xml name="requirements">
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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12 <requirements>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
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13 <requirement type="package" version="@TOOL_VERSION@">freyja</requirement>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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14 <yield/>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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15 </requirements>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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16 </xml>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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17 <xml name="version">
d4a1c2f9e843 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>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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19 </xml>
d4a1c2f9e843 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[
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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21 #if $usher_update_option.choice == 'update'
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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22 freyja update &&
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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23 #end if
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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24 ]]></token>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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25 <token name="@PREPROCESS_VCF_INPUT@"><![CDATA[
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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26 ln -s '$variants_file' 'variants_file.vcf' &&
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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27 ]]></token>
d4a1c2f9e843 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[
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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29 #if $variants_file.ext == 'vcf'
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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30 'variants_file.vcf'
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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31 #else
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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32 '$variants_file'
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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33 #end if
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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34 '$depth_file'
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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35 #if $eps
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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36 --eps '${eps}'
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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37 #end if
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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38 #if $meta
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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39 --meta '${meta}'
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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40 #end if
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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41 $confirmedonly
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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42 ]]></token>
d4a1c2f9e843 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[
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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44 #if $usher_update_option.choice == 'custom'
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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45 --barcodes '${usher_update_option.usher_barcodes}'
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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46 #end if
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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47 ]]></token>
d4a1c2f9e843 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[
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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49 echo '${plot_format.plot_title}' > plot_title.txt &&
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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50 echo '${plot_format.plot_intro}' > plot_intro.txt &&
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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51 freyja dash
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52 #if $need_aggregation.choice == 'no'
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53 '$tsv_aggregated'
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54 #else
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55 'aggregated.tsv'
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56 #end if
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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57 '$plot_format.csv_meta'
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58 plot_title.txt
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59 plot_intro.txt
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60 --output abundances_dashboard.html
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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61 ]]></token>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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62 <token name="@PLOT_COMMAND@"><![CDATA[
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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63 freyja plot
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64 #if $need_aggregation.choice == 'no'
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65 '$tsv_aggregated'
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66 #else
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67 'aggregated.tsv'
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68 #end if
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69 --output abundances_plot.pdf
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70 #if $plot_format.csv_meta
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71 --times '${plot_format.csv_meta}'
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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72 #end if
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73 #if $plot_format.interval == 'MS'
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74 --interval MS
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75 #else
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76 --interval D
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77 --windowsize 70
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78 #end if
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79 ]]></token>
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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80 <token name="@PLOT_AND_DASH_COMMAND@"><![CDATA[
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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81 #if $plot_format.choice == 'dash'
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82 @DASH_COMMAND@
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83 #else if $plot_format.choice == 'plot'
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84 freyja plot
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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85 #if $need_aggregation.choice == 'no'
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86 $tsv_aggregated
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87 #else
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88 aggregated.tsv
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89 #end if
d4a1c2f9e843 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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90 --output abundances_plot.pdf
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91 #if $plot_format.need_metadata.choice == 'yes'
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92 --times '${plot_format.need_metadata.csv_meta}'
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93 #if $plot_format.need_metadata.interval == 'MS'
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94 --interval MS
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95 #else
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96 --interval D
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97 --windowsize 70
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98 #end if
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99 #end if
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100 #else if $plot_format.choice == 'plot_and_dash'
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101 @DASH_COMMAND@ &&
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102 @PLOT_COMMAND@
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103 #end if
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104 ]]></token>
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105 <xml name="demixing_common_options">
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106 <param name="depth_file" type="data" format="tabular" label="Sequencing depth file"/>
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107 <conditional name="usher_update_option">
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108 <param name="choice" type="select" label="Source of UShER barcodes data"
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109 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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110 <option value="repo" selected="true">Use data shipped with the tool (can be
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111 outdated)
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112 </option>
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113 <option value="custom">Provide a custom barcodes file</option>
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114 <!--<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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115 </param>
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116 <when value="repo"/>
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117 <when value="custom">
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118 <param name="usher_barcodes" type="data" format="csv" label="UShER barcodes file"/>
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119 </when>
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120 <!--<when value="update" />-->
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121 </conditional>
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122 <param argument="--meta" type="data" format="json" optional="true"
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123 label="Custom lineage metadata file"
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124 help="For additional flexibility and reproducibility of analyses, a custom lineage-to-contellation mapping metadata file can be provided."/>
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125 <param argument="--eps" type="float" optional="true"
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126 label="Minimum lineage abundance tp include"
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127 help="e.g. 0.0001."/>
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128 <param argument="--confirmedonly" type="boolean" truevalue="--confirmedonly" falsevalue=""
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129 checked="false"
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130 label="Remove unconfirmed lineages from the analysis"
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131 help="If the UShER tree includes proposed lineages, the --confirmedonly flag removes unconfirmed lineages from the analysis."/>
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132 </xml>
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133 <token name="@HELP_HEADER@"><![CDATA[
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134 What it does
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135 ============
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136
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137 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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138
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139 General information
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140 ===================
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141
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142 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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143
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144 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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145 ]]></token>
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146 <xml name="citations">
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147 <citations>
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148 <citation type="doi">10.5281/zenodo.6585067</citation>
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149 </citations>
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150 </xml>
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151 </macros>