annotate pangolin.xml @ 25:ca337cce3888 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 7c0046582ccfc786f39ba071974e550aebee86af
author iuc
date Fri, 14 Oct 2022 23:50:44 +0000
parents 77402759b866
children 007ffbb11881
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1 <tool id="pangolin" name="Pangolin" version="@TOOL_VERSION@+galaxy0" profile="20.01">
0
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2 <description>Phylogenetic Assignment of Outbreak Lineages</description>
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3 <macros>
23
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4 <token name="@TOOL_VERSION@">4.1.2</token>
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5 <token name="@PANGOLIN_DATA_VERSION@">1.12</token>
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6 <token name="@CONSTELLATIONS_VERSION@">0.1.10</token>
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7 <token name="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@">4</token>
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8 <!-- a regex describing the scorpio versions that this wrapper version
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9 is backwards-compatible with; can be used with the min_scorpio_version
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10 column of the constellations data table to offer only compatible
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11 versions of constellations data. -->
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12 <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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13 <xml name="usher_download_option">
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14 <when value="download">
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15 <param argument="--use-assignment-cache" type="boolean" truevalue="--use-assignment-cache" falsevalue="" label="Download and use also latest UShER assignment cache?"
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16 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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17 </when>
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18 </xml>
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19 <xml name="cached_usher_assignment_cache">
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20 <param name="assignment_cache_release" type="select" optional="true" label="Use corresponding UShER assignment cache?"
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21 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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22 <options from_data_table="pangolin_assignment">
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23 <column name="value" index="0" />
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24 <column name="description" index="1" />
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25 <column name="path" index="4" />
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26 <filter type="static_value" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@" />
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27 <filter type="param_value" ref="release" column="0" />
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28 </options>
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29 </param>
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30 </xml>
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31 <xml name="cached_pangolin_data">
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32 <when value="cached">
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33 <param name="release" label="Cached release of pangolin-data" type="select">
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34 <options from_data_table="pangolin_data">
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35 <column name="value" index="0" />
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36 <column name="description" index="1" />
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37 <column name="date" index="3" />
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38 <column name="path" index="4" />
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39 <filter type="sort_by" column="3" />
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40 <filter type="static_value" column="2" value="@MIN_COMPATIBLE_PANGOLIN_DATA_FORMAT@" />
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41 <validator type="no_options" message="No cached constellations release available" />
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42 </options>
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43 </param>
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44 <yield />
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45 </when>
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46 </xml>
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47 <xml name="pangolin_data_sources">
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48 <conditional name="pangolin_data">
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49 <param name="source" type="select" label="Version of pangolin-data to use">
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50 <option value="default">Use pangolin-data version (v@PANGOLIN_DATA_VERSION@) shipped with this version of the tool</option>
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51 <option value="cached">Use specific pangolin-data version cached on this Galaxy server</option>
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52 <option value="download">Download latest available pangolin-data version from web</option>
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53 </param>
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54 <when value="default" />
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55 <yield />
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56 </conditional>
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57 </xml>
0
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58 </macros>
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59 <requirements>
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60 <requirement type="package" version="@TOOL_VERSION@">pangolin</requirement>
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61 <!-- Pin also the versions of all core dependencies - the ones
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62 reported with the all-versions option of pangolin plus ucsc-fatovcf,
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63 which the command is intended to report but currently cannot for
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64 technical reasons - to the versions you'd get installed in an unpinned
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65 conda install of pangolin at the time of release of this wrapper
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66 version! By turning these dependencies into explicit requirements the
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67 requirements section of the tool interface becomes the equivalent of
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68 the all-versions option as long as the user doesn't update the data
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69 dependencies.
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70 Wrapper updates are **explicitly encouraged** when new dependency
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71 versions become available. Also, please check for updated dependencies
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72 when updating the wrapper for other reasons. -->
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73 <requirement type="package" version="0.3.17">scorpio</requirement>
22
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74 <requirement type="package" version="@PANGOLIN_DATA_VERSION@">pangolin-data</requirement>
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75 <requirement type="package" version="@CONSTELLATIONS_VERSION@">constellations</requirement>
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76 <requirement type="package" version="0.5.6">usher</requirement>
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77 <requirement type="package" version="1.1.0">gofasta</requirement>
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78 <requirement type="package" version="426">ucsc-fatovcf</requirement>
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79 <requirement type="package" version="2.24">minimap2</requirement>
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80 <!-- wrapper-specific requirements to turn pangolin's native
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81 comma-separated output into tab-separated one and to truncate
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82 pangolin's all-versions output. -->
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83 <requirement type="package" version="0.23.0">csvtk</requirement>
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84 <requirement type="package" version="3.4">grep</requirement>
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85 </requirements>
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86 <version_command><![CDATA[pangolin --version]]></version_command>
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87 <command detect_errors="exit_code"><![CDATA[
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88 ## Prepare a pangolin datadir if required:
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89 #if str($engine.pangolin_data.source) != 'default' or str($constellations.source) != 'default':
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90 ## for at least one of pangolin-data and constellations we need to
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91 ## provide a non-conda env version through a datadir
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92 mkdir datadir &&
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93 #if str($engine.pangolin_data.source) == 'download' or str($constellations.source) == 'download':
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94 ## If "download latest from web" got requested for any data component,
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95 ## we can make use of pangolin --update-data to do the job for us.
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96 ## However, this would download updated versions of *all* data
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97 ## packages into our datadir, while the user may have asked for
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98 ## just a specific one. To avoid this, we set up a fake package
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99 ## with very high version number in the datadir to prevent
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100 ## unwanted component updates. After updating the rest of the
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101 ## data, we remove the fake package again.
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102 #if str($engine.pangolin_data.source) != 'download':
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103 mkdir datadir/pangolin_data &&
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104 echo '__version__ = "999"' > datadir/pangolin_data/__init__.py &&
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105 #end if
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106 #if str($constellations.source) != 'download':
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107 mkdir datadir/constellations &&
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108 ## constellations versions start with a 'v'!
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109 echo '__version__ = "v999"' > datadir/constellations/__init__.py &&
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110 #end if
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111 ## download updated packages discarding stdout because we
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112 ## output final package versions separately below and because
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113 ## it would contain our fake package versions
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114 pangolin --update-data --datadir datadir 2&> /dev/null &&
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115 #if str($engine.pangolin_data.source) != 'download':
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116 rm -r datadir/pangolin_data &&
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117 #end if
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118 #if str($constellations.source) != 'download':
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119 rm -r datadir/constellations &&
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120 #end if
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121 #end if
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122 #if str($engine.analysis_mode) == 'usher' and str($engine.pangolin_data.source) == 'download':
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123 #if $engine.pangolin_data.use_assignment_cache:
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124 ## We need to download also the latest UShER assignment cache data.
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125 ## Since v4.1 pangolin's
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126 ## --add-assignment-cache/--use-assignment-cache options respect
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127 ## --datadir so we can use them directly.
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128 pangolin --datadir datadir --add-assignment-cache &&
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129 #end if
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130 #end if
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131 ## Handle data components to be taken from data tables
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132 ## The folder structure pointed to by the data tables can be used
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133 ## as is except that cannot symlink the folders themselves since
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134 ## pangolin inspects them using os.walk with the default
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135 ## `followlinks=False`.
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136 ## Since data table versions of data packages can be older than
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137 ## the versions installed in the wrapper environment, we need to
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138 ## use pangolin's --use-old-datadir option to actually have them
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139 ## used.
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140 #set $use_old_datadir = ''
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141 #if str($engine.pangolin_data.source) == 'cached':
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142 #set $use_old_datadir = '--use-old-datadir'
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143 cp -rs '${engine.pangolin_data.release.fields.path}' datadir/pangolin_data &&
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144 #if str($engine.analysis_mode) == 'usher' and $engine.pangolin_data.assignment_cache_release:
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145 cp -rs '${engine.pangolin_data.assignment_cache_release.fields.path}' datadir/pangolin_assignment &&
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146 #end if
22
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147 #end if
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148 #if str($constellations.source) == 'cached':
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149 #set $use_old_datadir = '--use-old-datadir'
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150 cp -rs '${constellations.release.fields.path}' datadir/constellations &&
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151 #end if
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152 ## Report all data package versions that will be used in this run of the tool
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153 echo "Running pangolin with the following possibly updated data packages:" &&
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154 pangolin --datadir datadir $use_old_datadir --all-versions | grep -E "pangolin-data|assignment|constellations" &&
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155 #end if
23
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156 ## Since v4.0.6 pangolin can handle compressed fasta as input,
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157 ## but recognizes file type by suffix.
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158 #if $input1.is_of_type('fasta.gz'):
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159 #set $query = 'query.fa.gz'
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160 #else:
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161 #set $query = 'query.fa'
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162 #end if
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163 ln -s '$input1' $query &&
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164 ## Finally run the pangolin analysis
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165 pangolin
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166 --threads \${GALAXY_SLOTS:-1}
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167 --tempdir "\${TMPDIR:-.}"
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168 #if str($engine.pangolin_data.source) != 'default' or str($constellations.source) != 'default':
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169 --datadir datadir $use_old_datadir
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170 #end if
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171 --analysis-mode $engine.analysis_mode
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172 #if str($engine.analysis_mode) == 'usher':
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173 #if str($engine.pangolin_data.source) == 'download':
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174 $engine.pangolin_data.use_assignment_cache
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175 #else if str($engine.pangolin_data.source) == 'cached':
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176 #if $engine.pangolin_data.assignment_cache_release:
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177 --use-assignment-cache
19
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178 #end if
22
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179 #end if
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180 #end if
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181 #if $alignment:
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182 $alignment --alignment-file '$align1'
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183 #end if
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184 --outfile report.csv
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185 --max-ambig $max_ambig
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186 --min-length $min_length
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187 $expanded_lineage
23
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188 $query
22
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189 && csvtk csv2tab report.csv
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190 #if not $include_header:
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191 | tail -n+2
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192 #end if
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193 > '$output1'
0
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194 ]]></command>
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195 <inputs>
23
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196 <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" />
19
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197 <conditional name="engine">
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198 <param argument="--analysis-mode" type="select" label="Analysis mode"
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199 help="The analysis engine to use for lineage assignment. UShER is considered more accurate, but pangoLEARN is faster">
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200 <option value="usher">UShER</option>
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201 <option value="pangolearn">pangoLEARN</option>
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202 </param>
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203 <when value="usher">
22
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204 <expand macro="pangolin_data_sources">
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205 <expand macro="cached_pangolin_data">
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206 <expand macro="cached_usher_assignment_cache" />
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207 </expand>
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208 <expand macro="usher_download_option" />
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209 </expand>
19
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210 </when>
22
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211 <when value="pangolearn">
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212 <expand macro="pangolin_data_sources">
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213 <expand macro="cached_pangolin_data" />
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214 <when value="download" />
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215 </expand>
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216 </when>
19
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217 </conditional>
22
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218 <conditional name="constellations">
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219 <param name="source" type="select" label="Version of constellations to use">
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220 <option value="default">Use constellations version (v@CONSTELLATIONS_VERSION@) shipped with this version of the tool</option>
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221 <option value="cached">Use specific constellations version cached on this Galaxy server</option>
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222 <option value="download">Download latest available constellations version from web</option>
1
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223 </param>
22
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224 <when value="default" />
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225 <when value="cached">
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226 <param name="release" label="Cached constellations release" type="select">
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227 <options from_data_table="pangolin_constellations">
1
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228 <column name="value" index="0" />
22
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229 <column name="description" index="1" />
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230 <column name="date" index="3" />
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231 <column name="path" index="4" />
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232 <filter type="sort_by" column="3" />
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233 <filter type="regexp" column="2" value="@COMPATIBLE_SCORPIO_DATA_FORMAT@" />
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234 <validator type="no_options" message="No cached constellations release available" />
1
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235 </options>
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236 </param>
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237 </when>
22
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238 <when value="download" />
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239 </conditional>
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240 <param argument="--alignment" type="boolean" truevalue="--alignment" falsevalue="" label="Output multiple sequence alignment of input sequences" />
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241 <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" />
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242 <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." />
19
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243 <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." />
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244 <param name="include_header" type="boolean" truevalue="true" falsevalue="false" label="Include header line in output file" />
0
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245 </inputs>
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246 <outputs>
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247 <data name="output1" format="tabular" label="pangolin on ${on_string}">
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248 <actions>
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249 <conditional name="expanded_lineage">
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250 <when value="">
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251 <!-- default columns -->
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252 <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" />
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253 </when>
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diff changeset
254 <when value="--expanded-lineage">
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
255 <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" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
256 </when>
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
257 </conditional>
0
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
258 </actions>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
259 </data>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
260 <data name="align1" format="fasta" label="pangolin alignment on ${on_string}">
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
261 <filter>alignment</filter>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
262 </data>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
263 </outputs>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
264 <tests>
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
265 <test expect_num_outputs="1">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
266 <param name="input1" value="test1.fasta"/>
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
267 <conditional name="engine">
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
268 <!-- Test only the default UShER mode for now since the
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
269 pangolearn random forest model uses too much memory
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
270 see https://github.com/cov-lineages/pangolin/issues/395
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
271 <param name="analysis_mode" value="pangolearn" />
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
272 -->
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
273 <conditional name="pangolin_data">
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
274 <param name="source" value="default" />
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
275 </conditional>
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
276 </conditional>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
277 <output name="output1" ftype="tabular">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
278 <assert_contents>
14
83a69484cb87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 402a11a20ec3f724dfe0b1a4bc60d806e77c1b3d"
iuc
parents: 13
diff changeset
279 <has_text_matching expression="B\.1\.1\t\d\.\d" />
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
280 <has_text text="pass" />
4
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
281 <has_n_lines n="1" />
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
282 </assert_contents>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
283 </output>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
284 </test>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
285 <test expect_num_outputs="1">
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
286 <param name="input1" value="test1.fasta"/>
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
287 <conditional name="engine">
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
288 <conditional name="pangolin_data">
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
289 <param name="source" value="download" />
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
290 </conditional>
4
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
291 </conditional>
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
292 <output name="output1" ftype="tabular">
42126b414951 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
293 <assert_contents>
14
83a69484cb87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 402a11a20ec3f724dfe0b1a4bc60d806e77c1b3d"
iuc
parents: 13
diff changeset
294 <has_text_matching expression="B\.1\.1.*\t\d\.\d\t*PUSHER" />
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
295 <has_text text="pass" />
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
296 <has_n_lines n="1" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
297 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
298 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
299 </test>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
300 <test expect_num_outputs="2">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
301 <param name="input1" value="test1.fasta" />
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
302 <conditional name="engine">
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
303 <!-- Test only the default UShER mode for now since the
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
304 pangolearn random forest model uses too much memory
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
305 see https://github.com/cov-lineages/pangolin/issues/395
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
306 <param name="analysis_mode" value="pangolearn" />
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
307 -->
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
308 <conditional name="pangolin_data">
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
309 <param name="source" value="download" />
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
310 </conditional>
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
311 </conditional>
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
312 <param name="alignment" value="--alignment" />
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
313 <output name="output1" ftype="tabular">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
314 <assert_contents>
14
83a69484cb87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 402a11a20ec3f724dfe0b1a4bc60d806e77c1b3d"
iuc
parents: 13
diff changeset
315 <has_text_matching expression="B\.1\.1\t\d\.\d" />
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
316 <has_text text="pass" />
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
317 <has_n_lines n="1" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
318 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
319 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
320 <output name="align1" file="aln1.fasta" ftype="fasta">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
321 <assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
322 <has_text text="Consensus_EB232-crude-prep_S297" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
323 <has_n_lines n="2" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
324 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
325 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
326 </test>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
327 <!-- test include-header option -->
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
328 <test expect_num_outputs="1">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
329 <param name="input1" value="multiple_alignment.fasta.gz"/>
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
330 <conditional name="engine">
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
331 <!-- Test only the default UShER mode for now since the
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
332 pangolearn random forest model uses too much memory
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
333 see https://github.com/cov-lineages/pangolin/issues/395
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
334 <param name="analysis_mode" value="pangolearn" />
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
335 -->
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
336 <conditional name="pangolin_data">
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
337 <param name="source" value="default" />
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
338 </conditional>
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
339 </conditional>
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
340 <param name="include_header" value="true" />
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
341 <output name="output1" ftype="tabular">
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
342 <assert_contents>
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
343 <has_text text="pangolin_version" />
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
344 <has_text text="lineage" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
345 <has_text text="Serbia" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
346 <has_text text="Poland" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
347 <has_text text="USA" />
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
348 <has_n_lines n="35" />
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
349 <has_n_columns n="16" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
350 </assert_contents>
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
351 </output>
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
352 </test>
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
353 <!-- test with extra expanded_lineage column -->
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
354 <test expect_num_outputs="1">
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
355 <param name="input1" value="multiple_alignment.fasta.gz"/>
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
356 <conditional name="engine">
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
357 <!-- Test only the default UShER mode for now since the
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
358 pangolearn random forest model uses too much memory
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
359 see https://github.com/cov-lineages/pangolin/issues/395
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
360 <param name="analysis_mode" value="pangolearn" />
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
361 -->
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
362 <conditional name="pangolin_data">
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
363 <param name="source" value="default" />
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
364 </conditional>
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
365 </conditional>
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
366 <param name="expanded_lineage" value="true" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
367 <param name="include_header" value="true" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
368 <output name="output1" ftype="tabular">
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
369 <assert_contents>
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
370 <has_text text="pangolin_version" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
371 <has_text text="lineage" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
372 <has_text text="expanded_lineage" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
373 <has_text text="Serbia" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
374 <has_text text="Poland" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
375 <has_text text="USA" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
376 <has_n_lines n="35" />
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
377 <has_n_columns n="17" />
3
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
378 </assert_contents>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
379 </output>
514a786baaa9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
380 </test>
0
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
381 </tests>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
382 <help><![CDATA[
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
383
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
384 **What it does**
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
385
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
386 `Pangolin <https://cov-lineages.org/pangolin.html>`_
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
387 (Phylogenetic Assignment of Named Global Outbreak LINeages) is used to assign a
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
388 SARS-CoV-2 genome sequence the most likely lineage based on the PANGO
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
389 nomenclature system.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
390
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
391 **Data sources/versioning and reproducibility**
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
392
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
393 Pangolin uses the
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
394 `pangolin-data <https://github.com/cov-lineages/pangolin-data>`_ repository as
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
395 a source of its required model, protobuf, designation hash and alias files, and
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
396 the `constellations <https://github.com/cov-lineages/constellations>`_
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
397 repository for `scorpio <https://github.com/cov-lineages/scorpio>`_ -based
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
398 assignment of lineages of concern.
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
399
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
400 The tool ships with copies of these two data packages, and using these shipped
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
401 versions is *recommended* for reproducibility (even across Galaxy servers) and
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
402 speed of job execution.
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
403
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
404 If your instance of Galaxy offers cached alternative versions of
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
405 `pangolin-data` and/or `constellations`, you will be able to use them instead
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
406 of the shipped versions, which can be useful to reproduce results obtained
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
407 earlier with previous versions of pangolin.
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
408
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
409 Finally, you have the option to *download the latest version* of each data
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
410 package at job runtime.
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
411
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
412 .. class:: warningmark
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
413
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
414 You can use this option as a workaround to get the most up-to-date lineage
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
415 assignments even before the next Galaxy tool update (or before an admin
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
416 installs new cached data versions on your server), but be aware of the
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
417 following limitations:
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
418
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
419 1. Using latest downloaded data package versions renders results hard to
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
420 reproduce (e.g. rerunning a corresponding job will cause also a fresh
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
421 data download, which may yield different data versions as in the intial
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
422 run).
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
423
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
424 2. Downloaded latest versions of the data packages may be incompatible
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
425 with the *pangolin* and *scorpio* version run by the tool, which can
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
426 result in failing tool runs, but occasionally also in harder to diagnose
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
427 lineage assignment issues.
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
428
0
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
429 .. class:: infomark
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
430
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
431 The exact combination of pangolin, inference engine (UShER/pangoLEARN),
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
432 scorpio, and data packages that was used for a particular run of the tool
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
433 can be extracted from the four "version" columns in the output (see below
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
434 for details).
16
ca0d8cf80567 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"
iuc
parents: 15
diff changeset
435
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a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
436 In addition, lineage assignment with pangolin can be affected by the exact
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
437 versions of additional underlying software. The packaged versions of all
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
438 relevant dependencies are listed in the *Requirements* section below. This
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
439 section is the equivalent to running `pangolin --all-versions` on the
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
440 command line except that the listed versions of *pangolin-data* and
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
441 *constellations* are the ones installed with pangolin and may have been
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
442 overridden with the versions reported in the corresponding output columns
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
443 at tool runtime.
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
444
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
445 **Output**
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
446
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
447 The main output of the tool is a tabular file with one line per input sequence
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
448 and with columns providing the
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
449 `following information <https://cov-lineages.org/resources/pangolin/output.html>`_:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
450
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
451 taxon:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
452 The name of the input sequence
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
453
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
454 lineage:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
455 The most likely lineage assigned to a given sequence based on the inference
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
456 engine used and the SARS-CoV-2 diversity designated.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
457 This assignment is sensitive to missing data at key sites.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
458
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
459 conflict:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
460 If a sequence can fit into more than one category, the conflict score will
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
461 be greater than 0 and reflect the number of categories the sequence could
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
462 fit into.
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
463 If the conflict score is 0, this means that within the current assignment
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
464 model / lineage tree there is only one category that the sequence could
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
465 plausibly be assigned to.
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
466
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
467 ambiguity_score:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
468 This score is a function of the quantity of missing data in a sequence.
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
469 It represents the proportion of relevant sites in a sequence which were
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
470 imputed to the reference values.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
471 A score of 1 indicates that no sites were imputed, while a score of 0
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
472 indicates that more sites were imputed than were not imputed.
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
473 This score only includes sites which are used by the assignment engine to
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
474 classify a sequence.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
475
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
476 scorpio_call:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
477 If a query is assigned a constellation by scorpio this call is output in
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
478 this column.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
479 The full set of constellations searched by default can be found at the
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
480 constellations repository.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
481
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
482 scorpio_support:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
483 The support score is the proportion of defining variants which have the
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
484 alternative allele in the sequence.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
485
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
486 scorpio_conflict:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
487 The conflict score is the proportion of defining variants which have the
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
488 reference allele in the sequence. Ambiguous/other non-ref/alt bases at each
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
489 of the variant positions contribute only to the denominators of these
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
490 scores.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
491
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
492 scorpio_notes:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
493 A notes column specific to the scorpio output.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
494
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
495 version:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
496 A version number that represents both the inference method and the
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
497 pangolin-data version number, which as of pangolin 4.0 corresponds to the
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
498 pango-designation version used to prepare the inference files. For example:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
499
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
500 PANGO-1.2 indicates an identical sequence has been previously designated
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
501 this lineage, and has so gone through manual curation.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
502 The number 1.2 indicates the version of pango-designation that this
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
503 assignment is based on. These hashes and pango-designation version are
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
504 bundled with the pangoLEARN and UShER models.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
505
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
506 PLEARN-1.2 indicates that this sequence is different from any previously
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
507 designated and that the pangoLEARN model was used as an inference engine to
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
508 predict the most likely lineage based on the given version of
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
509 pango-designation upon which the pangoLEARN model was trained.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
510
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
511 PUSHER-1.2 indicates that this sequence is different from any previously
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
512 designated and that UShER was used as an inference engine with fast tree
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
513 placement and parsimony-based lineage assignment, based on a guide tree
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
514 (protobuf) file built from the data in a given pango-designation release
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
515 version.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
516
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
517 pangolin_version:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
518 The version of pangolin software running.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
519
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
520 scorpio_version:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
521 The version of the scorpio software installed.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
522
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
523 constellation_version:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
524 The version of constellations that scorpio has used to curate the lineage
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
525 assignment.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
526
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
527 is_designated:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
528 A boolean (True/False) column indicating whether that particular sequence
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
529 has been offically designated a lineage (via pango-designation).
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
530
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
531 qc_status:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
532 Indicates whether the sequence passed the QC thresholds for minimum length
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
533 and maximum N content.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
534
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
535 qc_notes:
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
536 Notes specific to the QC checks run on the sequences.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
537
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
538 note:
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
539 If any conflicts arose during assignment, this field will output the
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
540 alternative assignments. If the sequence failed QC this field will describe
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
541 why.
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
542 If the sequence met the SNP thresholds for scorpio to call a constellation,
22
a2099fb98cdb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 21
diff changeset
543 it’ll describe the exact SNP counts of Alt, Ref and Amb (alternative,
19
abf6dbe8c9d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 18
diff changeset
544 reference and ambiguous) alleles for that call.
0
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
545 ]]></help>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
546 <citations>
8
3a656a4a43ed "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 5a3f70ab430c70b260dd6e0f5b6c53aed2ca5520"
iuc
parents: 7
diff changeset
547 <citation type="doi">10.1093/ve/veab064</citation>
0
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
548 </citations>
0ec813ad2910 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
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549 </tool>