Mercurial > repos > iuc > freyja_boot

annotate freyja_boot.xml @ 1:6afb807ede8f 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 05:50:03 +0000
parents 4d6fe132443a
children 3275124de1b0
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4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
iuc
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1 <tool id="freyja_boot" name="Freyja: Bootstrapping" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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2 profile="@PROFILE@">
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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3 <description>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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4 method
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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5 </description>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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6 <macros>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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7 <import>macros.xml</import>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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8 </macros>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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9 <expand macro="biotools"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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10 <expand macro="requirements"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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11 <expand macro="version"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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12 <command detect_errors="exit_code"><![CDATA[
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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13 @RUN_FREYJA_UPDATE_COMMAND@
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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14 @PREPROCESS_VCF_INPUT@
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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15 freyja boot
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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16 @STANDARD_INPUT_FOR_BOOT@
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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17 --nt \${GALAXY_SLOTS:-4}
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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18 #if $nb
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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19 --nb $nb
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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20 #end if
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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21 --output_base 'boot_output'
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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22 @CUSTOM_BARCODES_COMMAND@
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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23 $boxplot_pdf
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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24 ]]></command>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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25 <inputs>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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26 <param name="variants_file" type="data" format="tabular" label="Variants file"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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27 <expand macro="demixing_common_options"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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28 <param argument="--nb" type="integer" optional="true" label="Number of bootstraps"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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29 <param name="boxplot_pdf" argument="--boxplot pdf" type="boolean" truevalue="--boxplot pdf"
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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30 falsevalue=""
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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31 checked="false" label="Generate boxplot"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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32 </inputs>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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33 <outputs>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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34 <data name="boot_lineages" format="csv" label="${tool.name} on ${on_string}: Lineages"
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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35 from_work_dir="boot_output_lineages.csv"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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36 <data name="boot_summarized" format="csv" label="${tool.name} on ${on_string}: Summarized"
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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37 from_work_dir="boot_output_summarized.csv">
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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38 </data>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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39 <data name="boot_lineages_plot" format="pdf"
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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40 label="${tool.name} on ${on_string}: Lineages boxplot"
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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41 from_work_dir="boot_output_lineages.pdf">
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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42 <filter>boxplot_pdf</filter>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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43 </data>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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44 <data name="boot_summarized_plot" format="pdf"
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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45 label="${tool.name} on ${on_string}: Summarized boxplot"
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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46 from_work_dir="boot_output_summarized.pdf">
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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47 <filter>boxplot_pdf</filter>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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48 </data>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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49 </outputs>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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50 <tests>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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51 <!-- Test 01: test tsv input files and plots -->
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52 <test expect_num_outputs="4">
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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53 <conditional name="usher_update_option">
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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54 <param name="choice" value="repo"/>
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55 </conditional>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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56 <param name="variants_file" value="variants.tsv"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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57 <param name="depth_file" value="depths.tsv"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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58 <param name="confirmedonly" value="false"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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59 <param name="nb" value="10"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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60 <param name="boxplot_pdf" value="true"/>
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61 <output name="boot_lineages" ftype="csv">
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62 <assert_contents>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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63 <has_text text="B.1.617.2"/>
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64 </assert_contents>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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65 </output>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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66 <output name="boot_summarized" ftype="csv">
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67 <assert_contents>
1
6afb807ede8f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 26266f43c51f3f711ecd3a7dc6aea581a3b57fc5
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68 <has_text text="Del"/>
0
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69 </assert_contents>
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70 </output>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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71 <output name="boot_lineages_plot" ftype="pdf">
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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72 <assert_contents>
1
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73 <has_text text="Matplot"/>
0
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74 </assert_contents>
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75 </output>
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76 <output name="boot_summarized_plot" ftype="pdf">
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77 <assert_contents>
1
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78 <has_text text="Matplot"/>
0
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79 </assert_contents>
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80 </output>
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81 </test>
1
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82
0
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83 <!-- Test 02: test VCF input file -->
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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84 <test expect_num_outputs="2">
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85 <conditional name="usher_update_option">
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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86 <param name="choice" value="repo"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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87 </conditional>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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88 <param name="variants_file" value="test.vcf"/>
4d6fe132443a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
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89 <param name="depth_file" value="depths.tsv"/>
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90 <param name="confirmedonly" value="false"/>
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91 <param name="nb" value="10"/>
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92 <param name="boxplot_pdf" value="false"/>
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93 <output name="boot_lineages" ftype="csv">
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94 <assert_contents>
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95 <has_text text="B.1.617.2"/>
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96 </assert_contents>
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97 </output>
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98 <output name="boot_summarized" ftype="csv">
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99 <assert_contents>
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100 <has_text text="Delta"/>
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101 </assert_contents>
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102 </output>
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103 </test>
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104 </tests>
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105 <help><![CDATA[
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106 @HELP_HEADER@
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107
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108 Information about **freyja boot** method
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109 ========================================
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110
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111 A fast bootstrapping method for freyja.
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112
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113 Outputs
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114 =======
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115
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116 Bootstrapping method results:
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117
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118 1. Bootstrap lineages: the 0.025, 0.05,0.25,0.5 (median),0.75, 0.95, and 0.975 percentiles for each lineage;
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119 2. Bootstrap summarized: WHO designated VOI/VOC
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120
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121 ]]></help>
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122 <expand macro="citations"/>
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123 </tool>