annotate nextclade.xml @ 18:feb40665d7cd draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e72bef3964ce9d0c52ef2713d177684dfbee4cfb
author iuc
date Wed, 31 Aug 2022 16:40:29 +0000
parents 07ab9bd68a02
children 128ba8da994f
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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="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option>
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76 <option value="flu_h3n2_ha">Influenza A H3N2 HA</option>
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77 <option value="flu_vic_ha">Influenza B Victoria HA</option>
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78 <option value="flu_yam_ha">Influenza B Yamagata HA</option>
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79 <option value="MPXV">Monkeypox (All Clades)</option>
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80 <option value="hMPXV">Human Monkeypox (hMPXV)</option>
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81 <option value="hMPXV_B1">Human Monkeypox Clade B.1</option>
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82 </param>
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83 <conditional name="db">
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84 <param name="source" type="select" label="Version of database to use">
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parents: 16
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85 <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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86 <option value="download">Download latest available database version from web</option>
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parents: 16
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87 </param>
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parents: 16
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88 <when value="cached">
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89 <param name="release" label="Cached nextclade database release" type="select">
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90 <options from_data_table="nextclade">
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91 <column name="value" index="0" />
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92 <column name="description" index="2" />
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parents: 16
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93 <column name="date" index="4" />
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94 <column name="path" index="5" />
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95 <filter type="sort_by" column="4" />
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96 <filter type="param_value" ref="organism" column="1" />
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97 <filter type="regexp" column="3" value="@COMPATIBILITY_SPEC@" />
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98 </options>
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99 </param>
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100 </when>
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101 <when value="download"></when>
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102 </conditional>
0
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103 <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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104 <option value="report_json">JSON format report</option>
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105 <option value="report_tsv" selected="true">Tabular format report</option>
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106 <option value="output_tree">Auspice v2 tree file (JSON format)</option>
4
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107 <option value="output_fasta">Aligned sequences (FASTA format)</option>
0
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108 </param>
2
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109 <param name="include_header" type="boolean" label="Include header line in output file"
5
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110 truevalue="true" falsevalue="false" />
0
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111 <conditional name="adv">
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112 <param name="advanced_options" type="select" label="Use advanced options" >
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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">
18
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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>
1
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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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132 <actions>
17
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133 <action name="column_names" type="metadata" default="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,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" />
1
0f20ed06ed6c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit fd2b9ee5fee733c61c5db0618de96d19261dcb79"
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134 </actions>
0
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135 </data>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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136 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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137 <filter>outputs and "report_json" in outputs</filter>
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138 </data>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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139 <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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140 <filter>outputs and "output_tree" in outputs</filter>
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141 </data>
4
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142 <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA alignment)">
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143 <filter>outputs and "output_fasta" in outputs</filter>
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144 </data>
0
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145 </outputs>
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146 <tests>
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147 <test expect_num_outputs="1">
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148 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
17
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149 <conditional name="db">
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150 <param name="source" value="download" />
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151 </conditional>
0
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152 <param name="outputs" value="report_tsv" />
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
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153 <param name="organism" value="sars-cov-2" />
0
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154 <output name="report_tsv">
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155 <assert_contents>
17
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156 <has_n_columns n="66" />
0
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157 <has_text text="20A" />
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158 </assert_contents>
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159 </output>
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160 </test>
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161 <test expect_num_outputs="3">
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162 <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
163 <conditional name="db">
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
164 <param name="source" value="download" />
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
165 </conditional>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
166 <param name="outputs" value="report_tsv,report_json,output_tree" />
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
167 <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
168 <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
169 <assert_contents>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
170 <has_n_columns n="66" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
171 <has_text text="20A" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
172 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
173 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
174 <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
175 <assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
176 <has_text text='"pos": 240,' />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
177 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
178 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
179 <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
180 <assert_contents>
7
f6db3ce6ed1c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
iuc
parents: 6
diff changeset
181 <has_text text='"title": "QC Status"' />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
182 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
183 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
184 </test>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
185 <test expect_num_outputs="1">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
186 <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
187 <conditional name="db">
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
188 <param name="source" value="download" />
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
189 </conditional>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
190 <param name="outputs" value="report_tsv" />
5
0c46b95d60c3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit b565283c946796dfb3f613f52db6008d234ecedb"
iuc
parents: 4
diff changeset
191 <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
192 <conditional name="adv">
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
193 <param name="advanced_options" value="yes" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
194 <param name="input_qc_config" value="strict_qc.json" ftype="json" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
195 </conditional>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
196 <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
197 <assert_contents>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
198 <has_n_columns n="66" />
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
199 <has_text text="mediocre" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
200 </assert_contents>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
201 </output>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
202 </test>
13
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
203 <test expect_num_outputs="2">
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
204 <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
205 <conditional name="db">
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
206 <param name="source" value="download" />
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
207 </conditional>
13
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
208 <param name="outputs" value="report_tsv,output_fasta" />
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
209 <param name="organism" value="sars-cov-2" />
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
210 <conditional name="adv">
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
211 <param name="advanced_options" value="yes" />
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
212 <param name="include_reference" value="true" />
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
213 </conditional>
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
214 <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
215 <assert_contents>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
216 <has_n_columns n="66" />
13
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
217 <has_text text="mediocre" />
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
218 </assert_contents>
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
219 </output>
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
220 <output name="output_fasta" value="output_alignment.fasta" ftype="fasta" />
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
221 </test>
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
222 <test expect_num_outputs="1">
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
223 <param name="input_fasta" value="mpxv.fasta.gz" ftype="fasta.gz" />
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
224 <conditional name="db">
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
225 <param name="source" value="download" />
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
226 </conditional>
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
227 <param name="outputs" value="report_tsv" />
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
228 <param name="organism" value="MPXV" />
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
229 <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
230 <assert_contents>
18
feb40665d7cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e72bef3964ce9d0c52ef2713d177684dfbee4cfb
iuc
parents: 17
diff changeset
231 <has_n_columns n="67" />
17
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
232 <has_text text="hMPXV-1" />
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
233 </assert_contents>
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
234 </output>
07ab9bd68a02 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 2c63aeec74c260ccd9b2cdbbe1869bef2f3d5cda
iuc
parents: 16
diff changeset
235 </test>
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
236 </tests>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
237 <help><![CDATA[
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
238
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
239 .. class:: infomark
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
240
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
241 **What it does**
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
242
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
243 Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes.
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
244
13
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
245 For a description of nextclade's configuration files, see the `nextclade documentation <https://docs.nextstrain.org/projects/nextclade/en/latest/index.html>`_.
64be7ff9b97b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
iuc
parents: 8
diff changeset
246
0
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
247 **Input**
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
248
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
249 Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes.
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
250
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
parents:
diff changeset
251 **Output**
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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252
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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253 Outputs can include:
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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254
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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255 * A tabular format file with a report, one line per input sequence
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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256
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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257 * A JSON format file with the same information as is present in the tabular report
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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258
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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259 * An Auspice v2 tree file in JSON format
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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260
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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261 .. _Nextclade: https://github.com/nextstrain/nextclade
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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262
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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263 ]]></help>
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
iuc
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264 <expand macro="citations" />
615f484bdb4a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 52ba8fbf88f6c92b2811ace30ebd091b0800057a"
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265 </tool>