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comparison nextclade.xml @ 13:64be7ff9b97b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit ab4114a60ce5358ef2fbe9c7e8acbedd40c545d9"
author iuc
date Thu, 27 Jan 2022 14:04:45 +0000
parents 56b1a13d9680
children b60593baff7d
comparison
equal deleted inserted replaced
12:7004ce07621a 13:64be7ff9b97b
9 <requirement type="package" version="8.31">coreutils</requirement> 9 <requirement type="package" version="8.31">coreutils</requirement>
10 </requirements> 10 </requirements>
11 <version_command>nextclade --version-detailed</version_command> 11 <version_command>nextclade --version-detailed</version_command>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 nextclade dataset get -n '${organism}' -o db && 13 nextclade dataset get -n '${organism}' -o db &&
14 #set $input_qc_config = "db/qc.json" 14 nextclade run
15 #set $input_root_seq = "db/reference.fasta" 15 --input-fasta '${input_fasta}'
16 #set $input_tree = "db/tree.json" 16 --input-dataset db/
17 #set $input_gene_map = "db/genemap.gff" 17 #if $adv.advanced_options == 'yes'
18 #set $input_pcr_primers = "db/primers.csv"
19 #if str($adv.advanced_options) == "yes"
20 #if $adv.input_qc_config 18 #if $adv.input_qc_config
21 #set $input_qc_config = $adv.input_qc_config 19 --input-qc-config '$adv.input_qc_config'
22 #end if 20 #end if
23 #if $adv.input_root_seq 21 #if $adv.input_root_seq
24 #set $input_root_seq = $adv.input_root_seq 22 --input-root-seq '$adv.input_root_seq'
25 #end if 23 #end if
26 #if $adv.input_tree 24 #if $adv.input_tree
27 #set $input_tree = $adv.input_tree 25 --input-tree '$adv.input_tree'
28 #end if 26 #end if
29 #if $adv.input_gene_map 27 #if $adv.input_gene_map
30 #set $input_gene_map = $adv.input_gene_map 28 --input-gene-map '$adv.input_gene_map'
31 #end if 29 #end if
32 #if $adv.input_pcr_primers 30 #if $adv.input_pcr_primers
33 #set $input_pcr_primers = $adv.input_pcr_primers 31 --input-pcr-primers '$adv.input_pcr_primers'
34 #end if 32 #end if
35 #end if 33 #if $adv.input_virus_properties
36 nextclade 34 --input-virus-properties '$adv.input_virus_properties'
37 --input-fasta '${input_fasta}' 35 #end if
38 --input-qc-config '${input_qc_config}' 36 #end if
39 --input-root-seq '${input_root_seq}'
40 --input-tree '${input_tree}'
41 --input-gene-map '${input_gene_map}'
42 --input-pcr-primers '${input_pcr_primers}'
43 #if $outputs and "report_tsv" in $outputs 37 #if $outputs and "report_tsv" in $outputs
44 #if $include_header 38 #if $include_header
45 --output-tsv '$report_tsv' 39 --output-tsv '$report_tsv'
46 #else 40 #else
47 --output-tsv report.tsv 41 --output-tsv report.tsv
89 <param argument="--input-qc-config" name="input_qc_config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration" /> 83 <param argument="--input-qc-config" name="input_qc_config" type="data" label="Quality Control (QC) Config file" format="json" optional="true" help="QC config json file containing custom QC configuration" />
90 <param argument="--input-root-seq" name="input_root_seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" /> 84 <param argument="--input-root-seq" name="input_root_seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" />
91 <param argument="--input-tree" name="input_tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" /> 85 <param argument="--input-tree" name="input_tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" />
92 <param argument="--input-gene-map" name="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" /> 86 <param argument="--input-gene-map" name="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" />
93 <param argument="--input-pcr-primers" name="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" /> 87 <param argument="--input-pcr-primers" name="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" />
94 <param argument="--include-reference" name="include_reference" 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" /> 88 <param argument="--input-virus-properties" name="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." />
89 <param argument="--include-reference" name="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" />
95 </when> 90 </when>
96 <when value="no"> 91 <when value="no">
97 </when> 92 </when>
98 </conditional> 93 </conditional>
99 </inputs> 94 </inputs>
100 <outputs> 95 <outputs>
101 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)"> 96 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
102 <filter>outputs and "report_tsv" in outputs</filter> 97 <filter>outputs and "report_tsv" in outputs</filter>
103 <actions> 98 <actions>
104 <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,frameShifts,aaSubstitutions,aaDeletions,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,errors" /> 99 <action name="column_names" type="metadata" default="seqName,clade,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,errors" />
105 </actions> 100 </actions>
106 </data> 101 </data>
107 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)"> 102 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
108 <filter>outputs and "report_json" in outputs</filter> 103 <filter>outputs and "report_json" in outputs</filter>
109 </data> 104 </data>
119 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 114 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
120 <param name="outputs" value="report_tsv" /> 115 <param name="outputs" value="report_tsv" />
121 <param name="organism" value="sars-cov-2" /> 116 <param name="organism" value="sars-cov-2" />
122 <output name="report_tsv"> 117 <output name="report_tsv">
123 <assert_contents> 118 <assert_contents>
124 <has_n_columns n="53" /> 119 <has_n_columns n="62" />
125 <has_text text="20A" /> 120 <has_text text="20A" />
126 </assert_contents> 121 </assert_contents>
127 </output> 122 </output>
128 </test> 123 </test>
129 <test expect_num_outputs="3"> 124 <test expect_num_outputs="3">
130 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 125 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
131 <param name="outputs" value="report_tsv,report_json,output_tree" /> 126 <param name="outputs" value="report_tsv,report_json,output_tree" />
132 <param name="organism" value="sars-cov-2" /> 127 <param name="organism" value="sars-cov-2" />
133 <output name="report_tsv"> 128 <output name="report_tsv">
134 <assert_contents> 129 <assert_contents>
135 <has_n_columns n="53" /> 130 <has_n_columns n="62" />
136 <has_text text="20A" /> 131 <has_text text="20A" />
137 </assert_contents> 132 </assert_contents>
138 </output> 133 </output>
139 <output name="report_json"> 134 <output name="report_json">
140 <assert_contents> 135 <assert_contents>
155 <param name="advanced_options" value="yes" /> 150 <param name="advanced_options" value="yes" />
156 <param name="input_qc_config" value="strict_qc.json" ftype="json" /> 151 <param name="input_qc_config" value="strict_qc.json" ftype="json" />
157 </conditional> 152 </conditional>
158 <output name="report_tsv"> 153 <output name="report_tsv">
159 <assert_contents> 154 <assert_contents>
160 <has_n_columns n="53" /> 155 <has_n_columns n="62" />
161 <has_text text="mediocre" /> 156 <has_text text="mediocre" />
162 </assert_contents> 157 </assert_contents>
163 </output> 158 </output>
159 </test>
160 <test expect_num_outputs="2">
161 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
162 <param name="outputs" value="report_tsv,output_fasta" />
163 <param name="organism" value="sars-cov-2" />
164 <conditional name="adv">
165 <param name="advanced_options" value="yes" />
166 <param name="include_reference" value="true" />
167 </conditional>
168 <output name="report_tsv">
169 <assert_contents>
170 <has_n_columns n="62" />
171 <has_text text="mediocre" />
172 </assert_contents>
173 </output>
174 <output name="output_fasta" value="output_alignment.fasta" ftype="fasta" />
164 </test> 175 </test>
165 </tests> 176 </tests>
166 <help><![CDATA[ 177 <help><![CDATA[
167 178
168 .. class:: infomark 179 .. class:: infomark
169 180
170 **What it does** 181 **What it does**
171 182
172 Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes. 183 Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes.
184
185 For a description of nextclade's configuration files, see the `nextclade documentation <https://docs.nextstrain.org/projects/nextclade/en/latest/index.html>`_.
173 186
174 **Input** 187 **Input**
175 188
176 Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes. 189 Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes.
177 190