Mercurial > repos > iuc > nextclade

annotate nextclade.xml @ 19:128ba8da994f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
author iuc
date Sat, 08 Oct 2022 20:03:50 +0000
parents feb40665d7cd
children 4f6349228462
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1 <tool id="nextclade" name="Nextclade" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
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2 <description>Viral genome clade assignment, mutation calling, and sequence quality checks</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 <!-- sars-cov-2 and influenza databases are compatible with nextclade 1+, MPXV ones
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7 with nextclade 2+ but at time of writing this tool is for nextclade version 2,
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8 so the following regexp will select all databases known to be compatible with
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9 this tool and exclude any requiring a future nextclade version 3. -->
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10 <token name="@COMPATIBILITY_SPEC@"><![CDATA[(^1\..+$|^2\.[0-4](\..+)*$)]]></token>
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11 </macros>
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12 <requirements>
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13 <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
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14 <requirement type="package" version="9.0">coreutils</requirement>
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15 </requirements>
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16 <version_command>nextclade --version-detailed</version_command>
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17 <command detect_errors="exit_code"><![CDATA[
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18 #if $db.source == "cached"
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19 ln -s '${db.release.fields.path}' db &&
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20 #elif $db.source == "download"
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21 nextclade dataset get -n '${organism}' -o db &&
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22 #end if
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23 @QUERY_FASTA@
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24 nextclade run
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25 --input-dataset db/
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26 #if $adv.advanced_options == 'yes'
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27 #if $adv.input_qc_config
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28 --input-qc-config '$adv.input_qc_config'
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29 #end if
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30 #if $adv.input_root_seq
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31 --input-root-seq '$adv.input_root_seq'
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32 #end if
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33 #if $adv.input_tree
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34 --input-tree '$adv.input_tree'
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35 #end if
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36 #if $adv.input_gene_map
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37 --input-gene-map '$adv.input_gene_map'
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38 #end if
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39 #if $adv.input_pcr_primers
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40 --input-pcr-primers '$adv.input_pcr_primers'
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41 #end if
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42 #if $adv.input_virus_properties
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43 --input-virus-properties '$adv.input_virus_properties'
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44 #end if
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45 #end if
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46 #if $outputs and "report_tsv" in $outputs
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47 #if $include_header
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48 --output-tsv '$report_tsv'
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49 #else
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50 --output-tsv report.tsv
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51 #end if
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52 #end if
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53 #if $outputs and "report_json" in $outputs
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54 --output-json '${report_json}'
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55 #end if
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56 #if $outputs and "output_tree" in $outputs
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57 --output-tree '${output_tree}'
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58 #end if
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59 #if $outputs and "output_fasta" in $outputs
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60 --output-fasta "${output_fasta}"
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61 #if str($adv.advanced_options) == "yes"
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62 $adv.include_reference
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63 #end if
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64 #end if
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65 $query
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66 #if $outputs and "report_tsv" in $outputs and not $include_header
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67 && tail -n+2 report.tsv >'$report_tsv'
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68 #end if
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69 ]]></command>
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70 <inputs>
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71 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences"/>
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72 <param name="organism" type="select" label="Organism">
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73 <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
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74 <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option>
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75 <option value="sars-cov-2-21L">SARS-CoV-2 relative to BA.2</option>
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76 <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option>
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77 <option value="flu_h3n2_ha">Influenza A H3N2 HA</option>
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78 <option value="flu_vic_ha">Influenza B Victoria HA</option>
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79 <option value="flu_yam_ha">Influenza B Yamagata HA</option>
19
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80 <option value="MPXV">Monkeypox (All Clades - MPXV)</option>
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81 <option value="hMPXV">Human Monkeypox (hMPXV)</option>
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82 <option value="hMPXV_B1">Human Monkeypox Clade B.1 (hMPXV_B1)</option>
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parents: 18
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83 </param>
17
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parents: 16
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84 <conditional name="db">
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parents: 16
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85 <param name="source" type="select" label="Version of database to use">
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parents: 16
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86 <option value="cached" selected="true">Use specific database version cached on this Galaxy server</option>
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parents: 16
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87 <option value="download">Download latest available database version from web</option>
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parents: 16
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88 </param>
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parents: 16
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89 <when value="cached">
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parents: 16
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90 <param name="release" label="Cached nextclade database release" type="select">
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91 <options from_data_table="nextclade">
19
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parents: 18
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92 <column name="value" index="0"/>
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parents: 18
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93 <column name="description" index="2"/>
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parents: 18
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94 <column name="date" index="4"/>
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parents: 18
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95 <column name="path" index="5"/>
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parents: 18
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96 <filter type="sort_by" column="4"/>
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parents: 18
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97 <filter type="param_value" ref="organism" column="1"/>
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parents: 18
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98 <filter type="regexp" column="3" value="@COMPATIBILITY_SPEC@"/>
17
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parents: 16
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99 </options>
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parents: 16
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100 </param>
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parents: 16
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101 </when>
19
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parents: 18
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102 <when value="download"/>
17
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parents: 16
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103 </conditional>
0
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104 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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105 <option value="report_json">JSON format report</option>
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106 <option value="report_tsv" selected="true">Tabular format report</option>
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107 <option value="output_tree">Auspice v2 tree file (JSON format)</option>
4
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108 <option value="output_fasta">Aligned sequences (FASTA format)</option>
0
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109 </param>
19
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110 <param name="include_header" type="boolean" label="Include header line in output file" truevalue="true" falsevalue="false"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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111 <conditional name="adv">
19
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112 <param name="advanced_options" type="select" label="Use advanced options">
0
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113 <option value="yes">Yes</option>
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114 <option value="no" selected="true">No</option>
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115 </param>
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116 <when value="yes">
19
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117 <param argument="--input-qc-config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration"/>
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118 <param argument="--input-root-seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence"/>
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119 <param argument="--input-tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree"/>
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120 <param argument="--input-gene-map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes"/>
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121 <param argument="--input-pcr-primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites"/>
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122 <param argument="--input-virus-properties" type="data" label="Configuration and data specific to a pathogen" format="json" optional="true" help="For more info on the virus properties JSON file, see the Nextclade documentation."/>
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123 <param argument="--include-reference" truevalue="--include-reference" falsevalue="" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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124 </when>
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125 <when value="no">
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126 </when>
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127 </conditional>
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128 </inputs>
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129 <outputs>
19
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130 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
0
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131 <filter>outputs and "report_tsv" in outputs</filter>
1
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parents: 0
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132 <actions>
19
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133 <conditional name="organism">
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134 <expand macro="column_metadata" dataset_name="sars-cov-2" extra_columns="Nextclade_pango,"/>
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135 <expand macro="column_metadata" dataset_name="sars-cov-2-no-recomb" extra_columns="Nextclade_pango,"/>
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136 <expand macro="column_metadata" dataset_name="sars-cov-2-21L" extra_columns="Nextclade_pango,partiallyAliased,immune_escape,ace2_binding,"/>
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137 <expand macro="column_metadata" dataset_name="flu_h1n1pdm_ha"/>
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138 <expand macro="column_metadata" dataset_name="flu_h3n2_ha"/>
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139 <expand macro="column_metadata" dataset_name="flu_vic_ha"/>
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140 <expand macro="column_metadata" dataset_name="flu_yam_ha"/>
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141 <expand macro="column_metadata" dataset_name="MPXV" extra_columns="outbreak,lineage,"/>
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142 <expand macro="column_metadata" dataset_name="hMPXV" extra_columns="outbreak,lineage,"/>
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143 <expand macro="column_metadata" dataset_name="hMPXV_B1" extra_columns="outbreak,lineage,"/>
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144 </conditional>
1
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145 </actions>
0
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146 </data>
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147 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
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148 <filter>outputs and "report_json" in outputs</filter>
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149 </data>
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150 <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">
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151 <filter>outputs and "output_tree" in outputs</filter>
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152 </data>
4
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153 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA alignment)">
b74b9a7b3e3b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
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154 <filter>outputs and "output_fasta" in outputs</filter>
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155 </data>
0
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156 </outputs>
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157 <tests>
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158 <test expect_num_outputs="1">
19
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159 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
17
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160 <conditional name="db">
19
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161 <param name="source" value="download"/>
17
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162 </conditional>
19
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163 <param name="outputs" value="report_tsv"/>
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164 <param name="organism" value="sars-cov-2"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
165 <output name="report_tsv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
166 <assert_contents>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
167 <has_n_columns n="67"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
168 <has_text text="20A"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
169 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
170 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
171 </test>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
172 <test expect_num_outputs="3">
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
173 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
174 <conditional name="db">
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
175 <param name="source" value="download"/>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
176 </conditional>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
177 <param name="outputs" value="report_tsv,report_json,output_tree"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
178 <param name="organism" value="sars-cov-2"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
179 <output name="report_tsv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
180 <assert_contents>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
181 <has_n_columns n="67"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
182 <has_text text="20A"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
183 </assert_contents>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
184 <metadata name="column_names" value="seqName,clade,Nextclade_pango,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalAminoacidInsertions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,privateNucMutations.reversionSubstitutions,privateNucMutations.labeledSubstitutions,privateNucMutations.unlabeledSubstitutions,privateNucMutations.totalReversionSubstitutions,privateNucMutations.totalLabeledSubstitutions,privateNucMutations.totalUnlabeledSubstitutions,privateNucMutations.totalPrivateSubstitutions,frameShifts,aaSubstitutions,aaDeletions,aaInsertions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,coverage,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.frameShiftsIgnored,qc.frameShifts.totalFrameShiftsIgnored,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,isReverseComplement,failedGenes,warnings,errors"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
185 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
186 <output name="report_json">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
187 <assert_contents>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
188 <has_text text="&quot;pos&quot;: 240,"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
189 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
190 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
191 <output name="output_tree">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
192 <assert_contents>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
193 <has_text text="&quot;title&quot;: &quot;QC Status&quot;"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
194 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
195 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
196 </test>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
197 <test expect_num_outputs="1">
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
198 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
199 <conditional name="db">
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
200 <param name="source" value="download"/>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
201 </conditional>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
202 <param name="outputs" value="report_tsv"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
203 <param name="organism" value="sars-cov-2"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
204 <conditional name="adv">
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
205 <param name="advanced_options" value="yes"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
206 <param name="input_qc_config" value="strict_qc.json" ftype="json"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
207 </conditional>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
208 <output name="report_tsv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
209 <assert_contents>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
210 <has_n_columns n="67"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
211 <has_text text="mediocre"/>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
212 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
213 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
214 </test>
13
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
215 <test expect_num_outputs="2">
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
216 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
217 <conditional name="db">
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
218 <param name="source" value="download"/>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
219 </conditional>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
220 <param name="outputs" value="report_tsv,output_fasta"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
221 <param name="organism" value="sars-cov-2"/>
13
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
222 <conditional name="adv">
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
223 <param name="advanced_options" value="yes"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
224 <param name="include_reference" value="true"/>
13
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
225 </conditional>
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
226 <output name="report_tsv">
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
227 <assert_contents>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
228 <has_n_columns n="67"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
229 <has_text text="mediocre"/>
13
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
230 </assert_contents>
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
231 </output>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
232 <output name="output_fasta" value="output_alignment.fasta" ftype="fasta"/>
13
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
233 </test>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
234 <test expect_num_outputs="1">
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
235 <param name="input_fasta" value="mpxv.fasta.gz" ftype="fasta.gz"/>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
236 <conditional name="db">
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
237 <param name="source" value="download"/>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
238 </conditional>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
239 <param name="outputs" value="report_tsv"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
240 <param name="organism" value="MPXV"/>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
241 <output name="report_tsv">
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
242 <assert_contents>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
243 <has_n_columns n="68"/>
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
parents: 18
diff changeset
244 <has_text text="hMPXV-1"/>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
245 </assert_contents>
19
128ba8da994f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
iuc
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246 <metadata name="column_names" value="seqName,clade,outbreak,lineage,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalAminoacidInsertions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,privateNucMutations.reversionSubstitutions,privateNucMutations.labeledSubstitutions,privateNucMutations.unlabeledSubstitutions,privateNucMutations.totalReversionSubstitutions,privateNucMutations.totalLabeledSubstitutions,privateNucMutations.totalUnlabeledSubstitutions,privateNucMutations.totalPrivateSubstitutions,frameShifts,aaSubstitutions,aaDeletions,aaInsertions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,coverage,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.frameShiftsIgnored,qc.frameShifts.totalFrameShiftsIgnored,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,isReverseComplement,failedGenes,warnings,errors"/>
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247 </output>
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248 </test>
0
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249 </tests>
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250 <help><![CDATA[
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251
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252 .. class:: infomark
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253
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254 **What it does**
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255
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256 Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes.
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257
13
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258 For a description of nextclade's configuration files, see the `nextclade documentation <https://docs.nextstrain.org/projects/nextclade/en/latest/index.html>`_.
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259
0
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260 **Input**
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261
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262 Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes.
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263
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264 **Output**
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265
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266 Outputs can include:
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267
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268 * A tabular format file with a report, one line per input sequence
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269
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270 * A JSON format file with the same information as is present in the tabular report
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271
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272 * An Auspice v2 tree file in JSON format
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273
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274 .. _Nextclade: https://github.com/nextstrain/nextclade
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275
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276 ]]></help>
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277 <expand macro="citations"/>
0
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278 </tool>