Mercurial > repos > iuc > pangolin

annotate pangolin.xml @ 25:8d6b8f492cb2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
author iuc
date Sun, 15 Jan 2023 10:33:59 +0000
parents 28926e244e85
children bff9c9cce9c0
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21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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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>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
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3 <macros>
25
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4 <token name="@TOOL_VERSION@">4.1.3</token>
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
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5 <token name="@PANGOLIN_DATA_VERSION@">1.17</token>
21
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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
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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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>
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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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?"
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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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." />
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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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?"
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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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.">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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22 <options from_data_table="pangolin_assignment">
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23 <column name="value" index="0" />
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
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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>
21
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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>
21
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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>
25
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76 <requirement type="package" version="0.6.2">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="0.25.0">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
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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
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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
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178 #end if
21
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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
22
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188 $query
21
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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>
22
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196 <param type="data" name="input1" format="fasta,fasta.gz" label="Input FASTA File(s)" />
18
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197 <conditional name="engine">
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198 <param argument="--analysis-mode" type="select" label="Analysis mode"
25
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199 help="The analysis engine to use for lineage assignment. UShER is considered more accurate; pangoLEARN typically requires more memory, but might be faster in some cases.">
18
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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">
21
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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>
18
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210 </when>
21
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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>
18
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217 </conditional>
21
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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>
21
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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" />
21
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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>
21
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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." />
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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>
18
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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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parents: 17
diff changeset
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" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
253 </when>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
254 <when value="--expanded-lineage">
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
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" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
256 </when>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
257 </conditional>
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
258 </actions>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
259 </data>
b7099144a3c8 "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}">
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
261 <filter>alignment</filter>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
262 </data>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
263 </outputs>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
264 <tests>
25
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
265 <!-- Test only the default UShER mode for now since the
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
266 pangolearn random forest model uses too much memory
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
267 see https://github.com/cov-lineages/pangolin/issues/395
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
268 <test expect_num_outputs="1">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
269 <param name="input1" value="test1.fasta"/>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
270 <conditional name="engine">
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
271 <param name="analysis_mode" value="pangolearn" />
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
272 <conditional name="pangolin_data">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
273 <param name="source" value="default" />
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
274 </conditional>
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
275 </conditional>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
276 <output name="output1" ftype="tabular">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
277 <assert_contents>
13
25470784f134 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 402a11a20ec3f724dfe0b1a4bc60d806e77c1b3d"
iuc
parents: 11
diff changeset
278 <has_text_matching expression="B\.1\.1\t\d\.\d" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
279 <has_text text="pass" />
4
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
280 <has_n_lines n="1" />
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
281 </assert_contents>
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
282 </output>
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
283 </test>
25
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
284 -->
4
6b5a64c4cb34 "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">
6b5a64c4cb34 "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"/>
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
287 <conditional name="engine">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
288 <conditional name="pangolin_data">
25
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
289 <param name="source" value="default" />
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
290 </conditional>
4
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
291 </conditional>
6b5a64c4cb34 "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">
6b5a64c4cb34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit ab174c9f8cbfc741501068dfa4f6ccf229a54489"
iuc
parents: 3
diff changeset
293 <assert_contents>
25
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
294 <has_text_matching expression="B\.1\.1.*\t\d\.\d+\t*PUSHER" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
295 <has_text text="pass" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
296 <has_n_lines n="1" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
297 </assert_contents>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
298 </output>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
299 </test>
25
8d6b8f492cb2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d1c58058506d5eca398a43d8e5f98e59a2067739
iuc
parents: 22
diff changeset
300 <!-- test download and alignment options -->
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
301 <test expect_num_outputs="2">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
302 <param name="input1" value="test1.fasta" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
303 <conditional name="engine">
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
304 <!-- Test only the default UShER mode for now since the
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
305 pangolearn random forest model uses too much memory
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
306 see https://github.com/cov-lineages/pangolin/issues/395
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
307 <param name="analysis_mode" value="pangolearn" />
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
308 -->
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
309 <conditional name="pangolin_data">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
310 <param name="source" value="download" />
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
311 </conditional>
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
312 </conditional>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
313 <param name="alignment" value="--alignment" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
314 <output name="output1" ftype="tabular">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
315 <assert_contents>
13
25470784f134 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 402a11a20ec3f724dfe0b1a4bc60d806e77c1b3d"
iuc
parents: 11
diff changeset
316 <has_text_matching expression="B\.1\.1\t\d\.\d" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
317 <has_text text="pass" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
318 <has_n_lines n="1" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
319 </assert_contents>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
320 </output>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
321 <output name="align1" file="aln1.fasta" ftype="fasta">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
322 <assert_contents>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
323 <has_text text="Consensus_EB232-crude-prep_S297" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
324 <has_n_lines n="2" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
325 </assert_contents>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
326 </output>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
327 </test>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
328 <!-- test include-header option -->
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
329 <test expect_num_outputs="1">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
330 <param name="input1" value="multiple_alignment.fasta.gz"/>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
331 <conditional name="engine">
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
332 <!-- Test only the default UShER mode for now since the
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
333 pangolearn random forest model uses too much memory
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
334 see https://github.com/cov-lineages/pangolin/issues/395
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
335 <param name="analysis_mode" value="pangolearn" />
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
336 -->
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
337 <conditional name="pangolin_data">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
338 <param name="source" value="default" />
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iuc
parents: 20
diff changeset
339 </conditional>
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
340 </conditional>
18
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iuc
parents: 17
diff changeset
341 <param name="include_header" value="true" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
342 <output name="output1" ftype="tabular">
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
343 <assert_contents>
18
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iuc
parents: 17
diff changeset
344 <has_text text="pangolin_version" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
345 <has_text text="lineage" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
346 <has_text text="Serbia" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
347 <has_text text="Poland" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
348 <has_text text="USA" />
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
349 <has_n_lines n="35" />
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
350 <has_n_columns n="16" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
351 </assert_contents>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
352 </output>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
353 </test>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
354 <!-- test with extra expanded_lineage column -->
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
355 <test expect_num_outputs="1">
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
356 <param name="input1" value="multiple_alignment.fasta.gz"/>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
357 <conditional name="engine">
21
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iuc
parents: 20
diff changeset
358 <!-- Test only the default UShER mode for now since the
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
359 pangolearn random forest model uses too much memory
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
360 see https://github.com/cov-lineages/pangolin/issues/395
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
361 <param name="analysis_mode" value="pangolearn" />
21
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iuc
parents: 20
diff changeset
362 -->
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
363 <conditional name="pangolin_data">
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
364 <param name="source" value="default" />
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
365 </conditional>
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
366 </conditional>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
367 <param name="expanded_lineage" value="true" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
368 <param name="include_header" value="true" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
369 <output name="output1" ftype="tabular">
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
370 <assert_contents>
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
371 <has_text text="pangolin_version" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
372 <has_text text="lineage" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
373 <has_text text="expanded_lineage" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
374 <has_text text="Serbia" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
375 <has_text text="Poland" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
376 <has_text text="USA" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
377 <has_n_lines n="35" />
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
378 <has_n_columns n="17" />
3
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
379 </assert_contents>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
380 </output>
68e94cfc9e6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit e4e6f491964a162964882db4e53e36803ceaab9e"
iuc
parents: 1
diff changeset
381 </test>
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
382 </tests>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
383 <help><![CDATA[
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
384
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
385 **What it does**
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
386
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
387 `Pangolin <https://cov-lineages.org/pangolin.html>`_
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
388 (Phylogenetic Assignment of Named Global Outbreak LINeages) is used to assign a
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
389 SARS-CoV-2 genome sequence the most likely lineage based on the PANGO
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
390 nomenclature system.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
391
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
392 **Data sources/versioning and reproducibility**
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
393
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
394 Pangolin uses the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
395 `pangolin-data <https://github.com/cov-lineages/pangolin-data>`_ repository as
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
396 a source of its required model, protobuf, designation hash and alias files, and
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
397 the `constellations <https://github.com/cov-lineages/constellations>`_
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
398 repository for `scorpio <https://github.com/cov-lineages/scorpio>`_ -based
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
399 assignment of lineages of concern.
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
400
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
401 The tool ships with copies of these two data packages, and using these shipped
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
402 versions is *recommended* for reproducibility (even across Galaxy servers) and
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
403 speed of job execution.
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
404
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
405 If your instance of Galaxy offers cached alternative versions of
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
406 `pangolin-data` and/or `constellations`, you will be able to use them instead
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
407 of the shipped versions, which can be useful to reproduce results obtained
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
408 earlier with previous versions of pangolin.
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
409
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
410 Finally, you have the option to *download the latest version* of each data
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
411 package at job runtime.
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
412
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
413 .. class:: warningmark
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
414
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
415 You can use this option as a workaround to get the most up-to-date lineage
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
416 assignments even before the next Galaxy tool update (or before an admin
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
417 installs new cached data versions on your server), but be aware of the
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
418 following limitations:
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
419
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
420 1. Using latest downloaded data package versions renders results hard to
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
421 reproduce (e.g. rerunning a corresponding job will cause also a fresh
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
422 data download, which may yield different data versions as in the intial
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
423 run).
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
424
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
425 2. Downloaded latest versions of the data packages may be incompatible
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
426 with the *pangolin* and *scorpio* version run by the tool, which can
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
427 result in failing tool runs, but occasionally also in harder to diagnose
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
428 lineage assignment issues.
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
429
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
430 .. class:: infomark
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
diff changeset
431
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dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
432 The exact combination of pangolin, inference engine (UShER/pangoLEARN),
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
433 scorpio, and data packages that was used for a particular run of the tool
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
434 can be extracted from the four "version" columns in the output (see below
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
435 for details).
15
f8a93c0fe44d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit c180ed8ecef5956fb7dec68b947464b805fcea0b"
iuc
parents: 14
diff changeset
436
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
437 In addition, lineage assignment with pangolin can be affected by the exact
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
438 versions of additional underlying software. The packaged versions of all
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
439 relevant dependencies are listed in the *Requirements* section below. This
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
440 section is the equivalent to running `pangolin --all-versions` on the
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
441 command line except that the listed versions of *pangolin-data* and
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
442 *constellations* are the ones installed with pangolin and may have been
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
443 overridden with the versions reported in the corresponding output columns
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
444 at tool runtime.
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
445
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
446 **Output**
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
447
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
448 The main output of the tool is a tabular file with one line per input sequence
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
449 and with columns providing the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
450 `following information <https://cov-lineages.org/resources/pangolin/output.html>`_:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
451
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
452 taxon:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
453 The name of the input sequence
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
454
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
455 lineage:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
456 The most likely lineage assigned to a given sequence based on the inference
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
457 engine used and the SARS-CoV-2 diversity designated.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
458 This assignment is sensitive to missing data at key sites.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
459
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
460 conflict:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
461 If a sequence can fit into more than one category, the conflict score will
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
462 be greater than 0 and reflect the number of categories the sequence could
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
463 fit into.
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
464 If the conflict score is 0, this means that within the current assignment
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
465 model / lineage tree there is only one category that the sequence could
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
466 plausibly be assigned to.
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
467
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
468 ambiguity_score:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
469 This score is a function of the quantity of missing data in a sequence.
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
470 It represents the proportion of relevant sites in a sequence which were
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
471 imputed to the reference values.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
472 A score of 1 indicates that no sites were imputed, while a score of 0
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
473 indicates that more sites were imputed than were not imputed.
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
474 This score only includes sites which are used by the assignment engine to
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
475 classify a sequence.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
476
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
477 scorpio_call:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
478 If a query is assigned a constellation by scorpio this call is output in
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
479 this column.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
480 The full set of constellations searched by default can be found at the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
481 constellations repository.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
482
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
483 scorpio_support:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
484 The support score is the proportion of defining variants which have the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
485 alternative allele in the sequence.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
486
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
487 scorpio_conflict:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
488 The conflict score is the proportion of defining variants which have the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
489 reference allele in the sequence. Ambiguous/other non-ref/alt bases at each
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
490 of the variant positions contribute only to the denominators of these
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
491 scores.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
492
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
493 scorpio_notes:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
494 A notes column specific to the scorpio output.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
495
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
496 version:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
497 A version number that represents both the inference method and the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
498 pangolin-data version number, which as of pangolin 4.0 corresponds to the
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
499 pango-designation version used to prepare the inference files. For example:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
500
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
501 PANGO-1.2 indicates an identical sequence has been previously designated
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
502 this lineage, and has so gone through manual curation.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
503 The number 1.2 indicates the version of pango-designation that this
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
504 assignment is based on. These hashes and pango-designation version are
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
505 bundled with the pangoLEARN and UShER models.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
506
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
507 PLEARN-1.2 indicates that this sequence is different from any previously
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
508 designated and that the pangoLEARN model was used as an inference engine to
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
509 predict the most likely lineage based on the given version of
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
510 pango-designation upon which the pangoLEARN model was trained.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
511
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
512 PUSHER-1.2 indicates that this sequence is different from any previously
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
513 designated and that UShER was used as an inference engine with fast tree
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
514 placement and parsimony-based lineage assignment, based on a guide tree
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
515 (protobuf) file built from the data in a given pango-designation release
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
516 version.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
517
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
518 pangolin_version:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
519 The version of pangolin software running.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
520
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
521 scorpio_version:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
522 The version of the scorpio software installed.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
523
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
524 constellation_version:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
525 The version of constellations that scorpio has used to curate the lineage
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
526 assignment.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
527
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
528 is_designated:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
529 A boolean (True/False) column indicating whether that particular sequence
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
530 has been offically designated a lineage (via pango-designation).
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
531
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
532 qc_status:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
533 Indicates whether the sequence passed the QC thresholds for minimum length
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
534 and maximum N content.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
535
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
536 qc_notes:
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
537 Notes specific to the QC checks run on the sequences.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
538
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
539 note:
21
4f61b54ad91f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit d160f73f58eb515a2da4ba76096ed3d8b6c88bdc
iuc
parents: 20
diff changeset
540 If any conflicts arose during assignment, this field will output the
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
541 alternative assignments. If the sequence failed QC this field will describe
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
542 why.
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
543 If the sequence met the SNP thresholds for scorpio to call a constellation,
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iuc
parents: 20
diff changeset
544 it’ll describe the exact SNP counts of Alt, Ref and Amb (alternative,
18
dea0f466a07c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 98c0d716cbd1237ae735ce83e0153ee246abd5d8"
iuc
parents: 17
diff changeset
545 reference and ambiguous) alleles for that call.
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
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546 ]]></help>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
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547 <citations>
8
cf00be3d99c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit 5a3f70ab430c70b260dd6e0f5b6c53aed2ca5520"
iuc
parents: 7
diff changeset
548 <citation type="doi">10.1093/ve/veab064</citation>
0
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
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549 </citations>
b7099144a3c8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit aca98a23e13f05dd076a203e73f43ca90e349e21"
iuc
parents:
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550 </tool>