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annotate pangolin.xml @ 30:5f736365108b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin commit 2ca3f9ad1c61effb960c9ee627cd1b07c99a8b8f
author iuc
date Mon, 17 Nov 2025 12:56:52 +0000
parents f0fc9c4f00fe
children
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1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy2" profile="21.09">
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2 <description>Phylogenetic Assignment of Outbreak Lineages</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">4.3.4</token>
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5 <token name="@PANGOLIN_DATA_VERSION@">1.26</token>
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6 <token name="@CONSTELLATIONS_VERSION@">0.1.12</token>
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7 <!-- a regex describing the pangolin-data versions that this wrapper version
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8 is backwards-compatible with; can be used with the min_pangolin_version
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9 column of the pangolin_data and pangolin_assignment data table to offer
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10 only compatible versions of that data. -->
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11 <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@"><![CDATA[^4$|^4\.3$]]></token>
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12 <!-- pangolin-data versions >=1.20 do not contain pangoLEARN models anymore.
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13 This version of pangolin still supports pangolearn analysis mode, but only when using
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14 older versions of pangolin-data. -->
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15 <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT_FOR_PANGOLEARN@">4</token>
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16 <!-- a regex describing the scorpio versions that this wrapper version
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17 is backwards-compatible with; can be used with the min_scorpio_version
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18 column of the pangolin_constellations data table to offer only compatible
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19 versions of constellations data. -->
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20 <token name="@COMPATIBLE_SCORPIO_DATA_FORMAT@"><![CDATA[(^0\.[1-3]$|^0\.[0-2]\.\d+$|^0\.3\.\d$|^0\.3\.1[0-7]$|^0$)]]></token>
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21 <xml name="cached_usher_assignment_cache">
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22 <param name="assignment_cache_release" type="select" optional="true" label="Use corresponding UShER assignment cache?"
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23 help="If the server offers a copy of the UShER assignment cache along with the specified version of pangolin-data, you can select it here to speed up UShER lineage assignment. If no suitable assignment cache is available, it is perfectly fine to proceed without one, and the performance difference will only become obvious with very large numbers of samples.">
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24 <options from_data_table="pangolin_assignment">
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25 <column name="value" index="0" />
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26 <column name="description" index="1" />
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27 <column name="path" index="4" />
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28 <filter type="regexp" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@" />
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29 <filter type="param_value" ref="release" column="0" />
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30 </options>
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31 </param>
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32 </xml>
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33 </macros>
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34 <xrefs>
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35 <xref type="bio.tools">pangolin_cov-lineages</xref>
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36 </xrefs>
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37 <requirements>
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38 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
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39 <!-- Pin also the versions of all core dependencies - the ones
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40 reported with the all-versions option of pangolin and which have a
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41 direct impact on the lineage assignment process - to the versions
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42 you'd get installed in an unpinned conda install of pangolin at the
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43 time of release of this wrapper version!
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44 By turning these dependencies into explicit requirements the
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45 requirements section of the tool interface becomes the equivalent of
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46 the all-versions option as long as the user doesn't update the data
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47 dependencies.
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48 Wrapper updates are **explicitly encouraged** when new dependency
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49 versions become available. Also, please check for updated dependencies
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50 when updating the wrapper for other reasons. -->
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51 <requirement type="package" version="0.3.19">scorpio</requirement>
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52 <requirement type="package" version="1.36">pangolin-data</requirement>
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53 <requirement type="package" version="0.1.12">constellations</requirement>
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54 <requirement type="package" version="0.6.6">usher</requirement>
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55 <requirement type="package" version="1.2.3">gofasta</requirement>
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56 <requirement type="package" version="482">ucsc-fatovcf</requirement>
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57 <requirement type="package" version="2.30">minimap2</requirement>
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58 <!-- wrapper-specific requirements to turn pangolin's native
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59 comma-separated output into tab-separated one and to truncate
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60 pangolin's all-versions output. -->
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61 <requirement type="package" version="0.35.0">csvtk</requirement>
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62 <requirement type="package" version="3.12">grep</requirement>
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63 </requirements>
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64 <version_command><![CDATA[pangolin --version]]></version_command>
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65 <command detect_errors="exit_code"><![CDATA[
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66 ## Prepare a pangolin datadir if required:
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67 #if str($engine.pangolin_data.source) != 'default' or str($constellations.source) != 'default':
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68 ## for at least one of pangolin-data and constellations we need to
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69 ## provide a non-conda env version through a datadir
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70 mkdir datadir &&
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71 #if str($engine.pangolin_data.source) == 'download' or str($constellations.source) == 'download':
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72 ## If "download latest from web" got requested for any data component,
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73 ## we can make use of pangolin --update-data to do the job for us.
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74 ## However, this would download updated versions of *all* data
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75 ## packages into our datadir, while the user may have asked for
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76 ## just a specific one. To avoid this, we set up a fake package
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77 ## with very high version number in the datadir to prevent
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78 ## unwanted component updates. After updating the rest of the
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79 ## data, we remove the fake package again.
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80 #if str($engine.pangolin_data.source) != 'download':
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81 mkdir datadir/pangolin_data &&
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82 echo '__version__ = "999"' > datadir/pangolin_data/__init__.py &&
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de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
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83 #end if
21
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84 #if str($constellations.source) != 'download':
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85 mkdir datadir/constellations &&
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86 ## constellations versions start with a 'v'!
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87 echo '__version__ = "v999"' > datadir/constellations/__init__.py &&
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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88 #end if
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89 ## download updated packages discarding stdout because we
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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90 ## output final package versions separately below and because
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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91 ## it would contain our fake package versions
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92 pangolin --update-data --datadir datadir 2&> /dev/null &&
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93 #if str($engine.pangolin_data.source) != 'download':
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94 rm -r datadir/pangolin_data &&
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95 #end if
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96 #if str($constellations.source) != 'download':
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97 rm -r datadir/constellations &&
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98 #end if
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99 #end if
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100 #if str($engine.analysis_mode) == 'usher' and str($engine.pangolin_data.source) == 'download':
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101 #if $engine.pangolin_data.use_assignment_cache:
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102 ## We need to download also the latest UShER assignment cache data.
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103 ## Since v4.1 pangolin's
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104 ## --add-assignment-cache/--use-assignment-cache options respect
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105 ## --datadir so we can use them directly.
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106 pangolin --datadir datadir --add-assignment-cache &&
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107 #end if
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108 #end if
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109 ## Handle data components to be taken from data tables
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110 ## The folder structure pointed to by the data tables can be used
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111 ## as is except that cannot symlink the folders themselves since
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112 ## pangolin inspects them using os.walk with the default
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113 ## `followlinks=False`.
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114 ## Since data table versions of data packages can be older than
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115 ## the versions installed in the wrapper environment, we need to
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116 ## use pangolin's --use-old-datadir option to actually have them
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117 ## used.
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118 #set $use_old_datadir = ''
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119 #if str($engine.pangolin_data.source) == 'cached':
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120 #set $use_old_datadir = '--use-old-datadir'
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121 cp -rs '${engine.pangolin_data.release.fields.path}' datadir/pangolin_data &&
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122 #if str($engine.analysis_mode) == 'usher' and $engine.pangolin_data.assignment_cache_release:
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123 cp -rs '${engine.pangolin_data.assignment_cache_release.fields.path}' datadir/pangolin_assignment &&
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124 #end if
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125 #end if
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126 #if str($constellations.source) == 'cached':
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127 #set $use_old_datadir = '--use-old-datadir'
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128 cp -rs '${constellations.release.fields.path}' datadir/constellations &&
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129 #end if
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130 ## Report all data package versions that will be used in this run of the tool
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131 echo "Running pangolin with the following possibly updated data packages:" &&
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132 pangolin --datadir datadir $use_old_datadir --all-versions | grep -E "pangolin-data|assignment|constellations" &&
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133 #end if
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134 ## Since v4.0.6 pangolin can handle compressed fasta as input,
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135 ## but recognizes file type by suffix.
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136 #if $input1.is_of_type('fasta.gz'):
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137 #set $query = 'query.fa.gz'
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138 #else:
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139 #set $query = 'query.fa'
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140 #end if
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141 ln -s '$input1' $query &&
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142 ## Finally run the pangolin analysis
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143 pangolin
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144 --threads \${GALAXY_SLOTS:-1}
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145 --tempdir "\${TMPDIR:-.}"
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146 #if str($engine.pangolin_data.source) != 'default' or str($constellations.source) != 'default':
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147 --datadir datadir $use_old_datadir
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148 #end if
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149 --analysis-mode $engine.analysis_mode
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150 #if str($engine.analysis_mode) == 'usher':
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151 #if str($engine.pangolin_data.source) == 'download':
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152 $engine.pangolin_data.use_assignment_cache
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153 #else if str($engine.pangolin_data.source) == 'cached':
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154 #if $engine.pangolin_data.assignment_cache_release:
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155 --use-assignment-cache
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156 #end if
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157 #end if
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158 #end if
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159 #if $alignment:
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160 $alignment --alignment-file aln.fa
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161 #end if
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162 --outfile report.csv
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163 --max-ambig $max_ambig
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164 --min-length $min_length
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165 $expanded_lineage
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166 $query
21
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167 && csvtk csv2tab report.csv
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168 #if not $include_header:
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169 | tail -n+2
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170 #end if
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171 > '$output1'
0
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172 ]]></command>
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173 <inputs>
22
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174 <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" />
18
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175 <conditional name="engine">
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176 <param argument="--analysis-mode" type="select" label="Analysis mode"
26
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177 help="The analysis engine to use for lineage assignment. Note: In this version, UShER mode is implemented through the usher-sampled algorithm of UShER. If you prefer to run the original usher algorithm, please use version 4.1.3 of the tool.">
18
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178 <option value="usher">UShER</option>
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179 <option value="pangolearn">pangoLEARN</option>
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180 </param>
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181 <when value="usher">
27
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182 <conditional name="pangolin_data">
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183 <param name="source" type="select" label="Version of pangolin-data to use">
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184 <option value="default">Use pangolin-data version (v@PANGOLIN_DATA_VERSION@) shipped with this version of the tool</option>
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185 <option value="cached">Use specific pangolin-data version cached on this Galaxy server</option>
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186 <option value="download">Download latest available pangolin-data version from web</option>
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187 </param>
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188 <when value="default" />
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189 <when value="cached">
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190 <param name="release" label="Cached release of pangolin-data" type="select">
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191 <options from_data_table="pangolin_data">
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192 <column name="value" index="0" />
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193 <column name="description" index="1" />
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194 <column name="date" index="3" />
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195 <column name="path" index="4" />
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196 <filter type="sort_by" column="3" />
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197 <filter type="regexp" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@" />
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198 <validator type="no_options" message="No compatible cached pangolin-data release available" />
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199 </options>
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200 </param>
21
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201 <expand macro="cached_usher_assignment_cache" />
27
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202 </when>
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203 <when value="download">
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204 <param argument="--use-assignment-cache" type="boolean" truevalue="--use-assignment-cache" falsevalue="" label="Download and use also latest UShER assignment cache?"
b081d0817679 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit f93f921e3c2d0002ff0c152d90b9221533ad22e9
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205 help="Get the latest UShER assignment cache from the pangolin-assignment online repository and use it to speed up UShER lineage assignment. Note: Downloading the cached assignments will only pay off for large numbers of input samples." />
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206 </when>
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207 </conditional>
18
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208 </when>
21
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209 <when value="pangolearn">
27
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210 <conditional name="pangolin_data">
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211 <param name="source" type="select" label="Version of pangolin-data to use"
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212 help="Please note: pangoLEARN mode is considered deprecated and the underlying machine learning model has been removed from recent versions of pangolin-data. If you really still want to use this mode, you are restricted to the compatible historic pangolin-data versions cached on this Galaxy server.">
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213 <option value="cached">Use specific pangolin-data version cached on this Galaxy server</option>
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214 </param>
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215 <when value="cached">
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216 <param name="release" label="Cached release of pangolin-data" type="select">
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217 <options from_data_table="pangolin_data">
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218 <column name="value" index="0" />
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219 <column name="description" index="1" />
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220 <column name="date" index="3" />
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221 <column name="path" index="4" />
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222 <filter type="sort_by" column="3" />
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223 <filter type="static_value" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT_FOR_PANGOLEARN@" />
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224 <validator type="no_options" message="No compatible cached pangolin-data release available" />
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225 </options>
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226 </param>
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227 </when>
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228 </conditional>
21
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229 </when>
18
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230 </conditional>
21
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231 <conditional name="constellations">
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232 <param name="source" type="select" label="Version of constellations to use">
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233 <option value="default">Use constellations version (v@CONSTELLATIONS_VERSION@) shipped with this version of the tool</option>
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234 <option value="cached">Use specific constellations version cached on this Galaxy server</option>
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235 <option value="download">Download latest available constellations version from web</option>
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236 </param>
21
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237 <when value="default" />
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238 <when value="cached">
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239 <param name="release" label="Cached constellations release" type="select">
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240 <options from_data_table="pangolin_constellations">
1
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
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241 <column name="value" index="0" />
21
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parents: 20
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242 <column name="description" index="1" />
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243 <column name="date" index="3" />
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244 <column name="path" index="4" />
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245 <filter type="sort_by" column="3" />
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246 <filter type="regexp" column="2" value="@COMPATIBLE_SCORPIO_DATA_FORMAT@" />
27
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247 <validator type="no_options" message="No compatible cached constellations release available" />
1
de3ceb419d91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 1522bdb834ffab157d1ca25e6e74db21f62e3aae"
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248 </options>
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249 </param>
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250 </when>
21
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251 <when value="download" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
252 </conditional>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
253 <param argument="--alignment" type="boolean" truevalue="--alignment" falsevalue="" label="Output multiple sequence alignment of input sequences" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
254 <param argument="--max-ambig" type="float" value="0.3" min="0" max="1" label="Maximum proportion of Ns allowed" help="Maximum proportion of Ns allowed for pangolin to attempt assignment" />
19
8f984a286015 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 21834c24b94f942ed759bd7a2fcf0b3b4b5fd839"
iuc
parents: 18
diff changeset
255 <param argument="--min-length" type="integer" value="0" min="0" max="29903" label="Minimum query length allowed" help="Minimum query length allowed for pangolin to attempt assignment. Please note that in the current implementation this parameter is used to calculate an alternate value for the 'Maximum proportion of Ns allowed' parameter as 1-(minlen/reflen). The smaller of the two will be used." />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
256 <param argument="--expanded-lineage" type="boolean" truevalue="--expanded-lineage" falsevalue="" label="Add expanded lineage column to output" help="Optional expanded lineage information as defined in the alias.json file in pangolin-data can be appended as an additional column to the output." />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
257 <param name="include_header" type="boolean" truevalue="true" falsevalue="false" label="Include header line in output file" />
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
258 </inputs>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
259 <outputs>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
260 <data name="output1" format="tabular" label="pangolin on ${on_string}">
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
261 <actions>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
262 <conditional name="expanded_lineage">
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
263 <when value="">
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
264 <!-- default columns -->
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
265 <action name="column_names" type="metadata" default="taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
266 </when>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
267 <when value="--expanded-lineage">
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
268 <action name="column_names" type="metadata" default="taxon,lineage,conflict,ambiguity_score,scorpio_call,scorpio_support,scorpio_conflict,scorpio_notes,version,pangolin_version,scorpio_version,constellation_version,is_designated,qc_status,qc_notes,note,expanded_lineage" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
269 </when>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
270 </conditional>
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
271 </actions>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
272 </data>
27
b081d0817679 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit f93f921e3c2d0002ff0c152d90b9221533ad22e9
iuc
parents: 26
diff changeset
273 <data name="align1" format="fasta" from_work_dir="aln.fa" label="pangolin alignment on ${on_string}">
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
274 <filter>alignment</filter>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
275 </data>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
276 </outputs>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
277 <tests>
25
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
278 <!-- Test only the default UShER mode for now since the
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
279 pangolearn random forest model uses too much memory
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
280 see https://github.com/cov-lineages/pangolin/issues/395
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
281 <test expect_num_outputs="1">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
282 <param name="input1" value="test1.fasta"/>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
283 <conditional name="engine">
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
284 <param name="analysis_mode" value="pangolearn" />
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
285 <conditional name="pangolin_data">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
286 <param name="source" value="default" />
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
287 </conditional>
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
288 </conditional>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
289 <output name="output1" ftype="tabular">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
290 <assert_contents>
13
25470784f134 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 402a11a20ec3f724dfe0b1a4bc60d806e77c1b3d"
iuc
parents: 11
diff changeset
291 <has_text_matching expression="B\.1\.1\t\d\.\d" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
292 <has_text text="pass" />
4
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
293 <has_n_lines n="1" />
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
294 </assert_contents>
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
295 </output>
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
296 </test>
25
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
297 -->
4
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
298 <test expect_num_outputs="1">
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
299 <param name="input1" value="test1.fasta"/>
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
300 <conditional name="engine">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
301 <conditional name="pangolin_data">
25
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
302 <param name="source" value="default" />
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
303 </conditional>
4
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
304 </conditional>
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
305 <output name="output1" ftype="tabular">
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
306 <assert_contents>
25
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
307 <has_text_matching expression="B\.1\.1.*\t\d\.\d+\t*PUSHER" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
308 <has_text text="pass" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
309 <has_n_lines n="1" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
310 </assert_contents>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
311 </output>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
312 </test>
25
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
313 <!-- test download and alignment options -->
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
314 <test expect_num_outputs="2">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
315 <param name="input1" value="test1.fasta" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
316 <conditional name="engine">
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
317 <!-- Test only the default UShER mode for now since the
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
318 pangolearn random forest model uses too much memory
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
319 see https://github.com/cov-lineages/pangolin/issues/395
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
320 <param name="analysis_mode" value="pangolearn" />
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
321 -->
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
322 <conditional name="pangolin_data">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
323 <param name="source" value="download" />
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
324 </conditional>
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
325 </conditional>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
326 <param name="alignment" value="--alignment" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
327 <output name="output1" ftype="tabular">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
328 <assert_contents>
13
25470784f134 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 402a11a20ec3f724dfe0b1a4bc60d806e77c1b3d"
iuc
parents: 11
diff changeset
329 <has_text_matching expression="B\.1\.1\t\d\.\d" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
330 <has_text text="pass" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
331 <has_n_lines n="1" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
332 </assert_contents>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
333 </output>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
334 <output name="align1" file="aln1.fasta" ftype="fasta">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
335 <assert_contents>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
336 <has_text text="Consensus_EB232-crude-prep_S297" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
337 <has_n_lines n="2" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
338 </assert_contents>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
339 </output>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
340 </test>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
341 <!-- test include-header option -->
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
342 <test expect_num_outputs="1">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
343 <param name="input1" value="multiple_alignment.fasta.gz"/>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
344 <conditional name="engine">
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
345 <!-- Test only the default UShER mode for now since the
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
346 pangolearn random forest model uses too much memory
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
347 see https://github.com/cov-lineages/pangolin/issues/395
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
348 <param name="analysis_mode" value="pangolearn" />
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
349 -->
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
350 <conditional name="pangolin_data">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
351 <param name="source" value="default" />
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
352 </conditional>
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
353 </conditional>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
354 <param name="include_header" value="true" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
355 <output name="output1" ftype="tabular">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
356 <assert_contents>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
357 <has_text text="pangolin_version" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
358 <has_text text="lineage" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
359 <has_text text="Serbia" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
360 <has_text text="Poland" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
361 <has_text text="USA" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
362 <has_n_lines n="35" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
363 <has_n_columns n="16" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
364 </assert_contents>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
365 </output>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
366 </test>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
367 <!-- test with extra expanded_lineage column -->
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
368 <test expect_num_outputs="1">
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
369 <param name="input1" value="multiple_alignment.fasta.gz"/>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
370 <conditional name="engine">
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
371 <!-- Test only the default UShER mode for now since the
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
372 pangolearn random forest model uses too much memory
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
373 see https://github.com/cov-lineages/pangolin/issues/395
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
374 <param name="analysis_mode" value="pangolearn" />
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
375 -->
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
376 <conditional name="pangolin_data">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
377 <param name="source" value="default" />
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
378 </conditional>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
379 </conditional>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
380 <param name="expanded_lineage" value="true" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
381 <param name="include_header" value="true" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
382 <output name="output1" ftype="tabular">
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
383 <assert_contents>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
384 <has_text text="pangolin_version" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
385 <has_text text="lineage" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
386 <has_text text="expanded_lineage" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
387 <has_text text="Serbia" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
388 <has_text text="Poland" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
389 <has_text text="USA" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
390 <has_n_lines n="35" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
391 <has_n_columns n="17" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
392 </assert_contents>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
393 </output>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
394 </test>
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
395 </tests>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
396 <help><![CDATA[
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
397
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
398 **What it does**
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
399
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
400 `Pangolin <https://cov-lineages.org/pangolin.html>`_
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
401 (Phylogenetic Assignment of Named Global Outbreak LINeages) is used to assign a
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
402 SARS-CoV-2 genome sequence the most likely lineage based on the PANGO
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
403 nomenclature system.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
404
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
405 **Data sources/versioning and reproducibility**
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
406
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
407 Pangolin uses the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
408 `pangolin-data <https://github.com/cov-lineages/pangolin-data>`_ repository as
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
409 a source of its required model, protobuf, designation hash and alias files, and
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
410 the `constellations <https://github.com/cov-lineages/constellations>`_
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
411 repository for `scorpio <https://github.com/cov-lineages/scorpio>`_ -based
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
412 assignment of lineages of concern.
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
413
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
414 The tool ships with copies of these two data packages, and using these shipped
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
415 versions is *recommended* for reproducibility (even across Galaxy servers) and
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
416 speed of job execution.
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
417
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
418 If your instance of Galaxy offers cached alternative versions of
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
419 `pangolin-data` and/or `constellations`, you will be able to use them instead
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
420 of the shipped versions, which can be useful to reproduce results obtained
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
421 earlier with previous versions of pangolin.
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
422
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
423 Finally, you have the option to *download the latest version* of each data
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
424 package at job runtime.
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
425
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
426 .. class:: warningmark
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
427
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
428 You can use this option as a workaround to get the most up-to-date lineage
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
429 assignments even before the next Galaxy tool update (or before an admin
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
430 installs new cached data versions on your server), but be aware of the
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
431 following limitations:
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
432
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
433 1. Using latest downloaded data package versions renders results hard to
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
434 reproduce (e.g. rerunning a corresponding job will cause also a fresh
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
435 data download, which may yield different data versions as in the intial
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
436 run).
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
437
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
438 2. Downloaded latest versions of the data packages may be incompatible
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
439 with the *pangolin* and *scorpio* version run by the tool, which can
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
440 result in failing tool runs, but occasionally also in harder to diagnose
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
441 lineage assignment issues.
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dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
442
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
443 .. class:: infomark
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
444
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dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
445 The exact combination of pangolin, inference engine (UShER/pangoLEARN),
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
446 scorpio, and data packages that was used for a particular run of the tool
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
447 can be extracted from the four "version" columns in the output (see below
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
448 for details).
15
f8a93c0fe44d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"
iuc
parents: 14
diff changeset
449
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
450 In addition, lineage assignment with pangolin can be affected by the exact
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
451 versions of additional underlying software. The packaged versions of all
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
452 relevant dependencies are listed in the *Requirements* section below. This
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
453 section is the equivalent to running `pangolin --all-versions` on the
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
454 command line except that the listed versions of *pangolin-data* and
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
455 *constellations* are the ones installed with pangolin and may have been
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
456 overridden with the versions reported in the corresponding output columns
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
457 at tool runtime.
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
458
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
459 **Output**
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
460
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
461 The main output of the tool is a tabular file with one line per input sequence
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
462 and with columns providing the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
463 `following information <https://cov-lineages.org/resources/pangolin/output.html>`_:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
464
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
465 taxon:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
466 The name of the input sequence
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
467
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
468 lineage:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
469 The most likely lineage assigned to a given sequence based on the inference
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
470 engine used and the SARS-CoV-2 diversity designated.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
471 This assignment is sensitive to missing data at key sites.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
472
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
473 conflict:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
474 If a sequence can fit into more than one category, the conflict score will
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
475 be greater than 0 and reflect the number of categories the sequence could
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
476 fit into.
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
477 If the conflict score is 0, this means that within the current assignment
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
478 model / lineage tree there is only one category that the sequence could
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
479 plausibly be assigned to.
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
480
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
481 ambiguity_score:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
482 This score is a function of the quantity of missing data in a sequence.
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
483 It represents the proportion of relevant sites in a sequence which were
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
484 imputed to the reference values.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
485 A score of 1 indicates that no sites were imputed, while a score of 0
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
486 indicates that more sites were imputed than were not imputed.
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
487 This score only includes sites which are used by the assignment engine to
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
488 classify a sequence.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
489
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
490 scorpio_call:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
491 If a query is assigned a constellation by scorpio this call is output in
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
492 this column.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
493 The full set of constellations searched by default can be found at the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
494 constellations repository.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
495
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
496 scorpio_support:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
497 The support score is the proportion of defining variants which have the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
498 alternative allele in the sequence.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
499
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
500 scorpio_conflict:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
501 The conflict score is the proportion of defining variants which have the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
502 reference allele in the sequence. Ambiguous/other non-ref/alt bases at each
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
503 of the variant positions contribute only to the denominators of these
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
504 scores.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
505
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
506 scorpio_notes:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
507 A notes column specific to the scorpio output.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
508
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
509 version:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
510 A version number that represents both the inference method and the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
511 pangolin-data version number, which as of pangolin 4.0 corresponds to the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
512 pango-designation version used to prepare the inference files. For example:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
513
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
514 PANGO-1.2 indicates an identical sequence has been previously designated
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
515 this lineage, and has so gone through manual curation.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
516 The number 1.2 indicates the version of pango-designation that this
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
517 assignment is based on. These hashes and pango-designation version are
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
518 bundled with the pangoLEARN and UShER models.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
519
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
520 PLEARN-1.2 indicates that this sequence is different from any previously
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
521 designated and that the pangoLEARN model was used as an inference engine to
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
522 predict the most likely lineage based on the given version of
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
523 pango-designation upon which the pangoLEARN model was trained.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
524
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
525 PUSHER-1.2 indicates that this sequence is different from any previously
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
526 designated and that UShER was used as an inference engine with fast tree
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
527 placement and parsimony-based lineage assignment, based on a guide tree
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
528 (protobuf) file built from the data in a given pango-designation release
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
529 version.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
530
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
531 pangolin_version:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
532 The version of pangolin software running.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
533
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
534 scorpio_version:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
535 The version of the scorpio software installed.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
536
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
537 constellation_version:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
538 The version of constellations that scorpio has used to curate the lineage
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
539 assignment.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
540
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
541 is_designated:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
542 A boolean (True/False) column indicating whether that particular sequence
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
543 has been offically designated a lineage (via pango-designation).
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
544
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
545 qc_status:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
546 Indicates whether the sequence passed the QC thresholds for minimum length
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
547 and maximum N content.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
548
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
549 qc_notes:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
550 Notes specific to the QC checks run on the sequences.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
551
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
552 note:
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
553 If any conflicts arose during assignment, this field will output the
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
554 alternative assignments. If the sequence failed QC this field will describe
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
555 why.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
556 If the sequence met the SNP thresholds for scorpio to call a constellation,
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
557 it’ll describe the exact SNP counts of Alt, Ref and Amb (alternative,
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
558 reference and ambiguous) alleles for that call.
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
559 ]]></help>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
560 <citations>
8
cf00be3d99c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 5a3f70ab430c70b260dd6e0f5b6c53aed2ca5520"
iuc
parents: 7
diff changeset
561 <citation type="doi">10.1093/ve/veab064</citation>
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
562 </citations>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
563 </tool>