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comparison nextclade.xml @ 18:6f40b91cd1ac draft default tip

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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 20:02:02 +0000
parents f09378dd39b0
children
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17:f09378dd39b0 18:6f40b91cd1ac
66 #if $outputs and "report_tsv" in $outputs and not $include_header 66 #if $outputs and "report_tsv" in $outputs and not $include_header
67 && tail -n+2 report.tsv >'$report_tsv' 67 && tail -n+2 report.tsv >'$report_tsv'
68 #end if 68 #end if
69 ]]></command> 69 ]]></command>
70 <inputs> 70 <inputs>
71 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences" /> 71 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences"/>
72 <param name="organism" type="select" label="Organism"> 72 <param name="organism" type="select" label="Organism">
73 <option value="sars-cov-2" selected="true">SARS-CoV-2</option> 73 <option value="sars-cov-2" selected="true">SARS-CoV-2</option>
74 <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option> 74 <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option>
75 <option value="sars-cov-2-21L">SARS-CoV-2 relative to BA.2</option>
75 <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option> 76 <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option>
76 <option value="flu_h3n2_ha">Influenza A H3N2 HA</option> 77 <option value="flu_h3n2_ha">Influenza A H3N2 HA</option>
77 <option value="flu_vic_ha">Influenza B Victoria HA</option> 78 <option value="flu_vic_ha">Influenza B Victoria HA</option>
78 <option value="flu_yam_ha">Influenza B Yamagata HA</option> 79 <option value="flu_yam_ha">Influenza B Yamagata HA</option>
79 <option value="MPXV">Monkeypox (All Clades)</option> 80 <option value="MPXV">Monkeypox (All Clades - MPXV)</option>
80 <option value="hMPXV">Human Monkeypox (hMPXV)</option> 81 <option value="hMPXV">Human Monkeypox (hMPXV)</option>
81 <option value="hMPXV_B1">Human Monkeypox Clade B.1</option> 82 <option value="hMPXV_B1">Human Monkeypox Clade B.1 (hMPXV_B1)</option>
82 </param> 83 </param>
83 <conditional name="db"> 84 <conditional name="db">
84 <param name="source" type="select" label="Version of database to use"> 85 <param name="source" type="select" label="Version of database to use">
85 <option value="cached" selected="true">Use specific database version cached on this Galaxy server</option> 86 <option value="cached" selected="true">Use specific database version cached on this Galaxy server</option>
86 <option value="download">Download latest available database version from web</option> 87 <option value="download">Download latest available database version from web</option>
87 </param> 88 </param>
88 <when value="cached"> 89 <when value="cached">
89 <param name="release" label="Cached nextclade database release" type="select"> 90 <param name="release" label="Cached nextclade database release" type="select">
90 <options from_data_table="nextclade"> 91 <options from_data_table="nextclade">
91 <column name="value" index="0" /> 92 <column name="value" index="0"/>
92 <column name="description" index="2" /> 93 <column name="description" index="2"/>
93 <column name="date" index="4" /> 94 <column name="date" index="4"/>
94 <column name="path" index="5" /> 95 <column name="path" index="5"/>
95 <filter type="sort_by" column="4" /> 96 <filter type="sort_by" column="4"/>
96 <filter type="param_value" ref="organism" column="1" /> 97 <filter type="param_value" ref="organism" column="1"/>
97 <filter type="regexp" column="3" value="@COMPATIBILITY_SPEC@" /> 98 <filter type="regexp" column="3" value="@COMPATIBILITY_SPEC@"/>
98 </options> 99 </options>
99 </param> 100 </param>
100 </when> 101 </when>
101 <when value="download"></when> 102 <when value="download"/>
102 </conditional> 103 </conditional>
103 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true"> 104 <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true">
104 <option value="report_json">JSON format report</option> 105 <option value="report_json">JSON format report</option>
105 <option value="report_tsv" selected="true">Tabular format report</option> 106 <option value="report_tsv" selected="true">Tabular format report</option>
106 <option value="output_tree">Auspice v2 tree file (JSON format)</option> 107 <option value="output_tree">Auspice v2 tree file (JSON format)</option>
107 <option value="output_fasta">Aligned sequences (FASTA format)</option> 108 <option value="output_fasta">Aligned sequences (FASTA format)</option>
108 </param> 109 </param>
109 <param name="include_header" type="boolean" label="Include header line in output file" 110 <param name="include_header" type="boolean" label="Include header line in output file" truevalue="true" falsevalue="false"/>
110 truevalue="true" falsevalue="false" />
111 <conditional name="adv"> 111 <conditional name="adv">
112 <param name="advanced_options" type="select" label="Use advanced options" > 112 <param name="advanced_options" type="select" label="Use advanced options">
113 <option value="yes">Yes</option> 113 <option value="yes">Yes</option>
114 <option value="no" selected="true">No</option> 114 <option value="no" selected="true">No</option>
115 </param> 115 </param>
116 <when value="yes"> 116 <when value="yes">
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" /> 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"/>
118 <param argument="--input-root-seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" /> 118 <param argument="--input-root-seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence"/>
119 <param argument="--input-tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" /> 119 <param argument="--input-tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree"/>
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" /> 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"/>
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" /> 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"/>
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." /> 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."/>
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" /> 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"/>
124 </when> 124 </when>
125 <when value="no"> 125 <when value="no">
126 </when> 126 </when>
127 </conditional> 127 </conditional>
128 </inputs> 128 </inputs>
129 <outputs> 129 <outputs>
130 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)"> 130 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
131 <filter>outputs and "report_tsv" in outputs</filter> 131 <filter>outputs and "report_tsv" in outputs</filter>
132 <actions> 132 <actions>
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" /> 133 <conditional name="organism">
134 <expand macro="column_metadata" dataset_name="sars-cov-2" extra_columns="Nextclade_pango,"/>
135 <expand macro="column_metadata" dataset_name="sars-cov-2-no-recomb" extra_columns="Nextclade_pango,"/>
136 <expand macro="column_metadata" dataset_name="sars-cov-2-21L" extra_columns="Nextclade_pango,partiallyAliased,immune_escape,ace2_binding,"/>
137 <expand macro="column_metadata" dataset_name="flu_h1n1pdm_ha"/>
138 <expand macro="column_metadata" dataset_name="flu_h3n2_ha"/>
139 <expand macro="column_metadata" dataset_name="flu_vic_ha"/>
140 <expand macro="column_metadata" dataset_name="flu_yam_ha"/>
141 <expand macro="column_metadata" dataset_name="MPXV" extra_columns="outbreak,lineage,"/>
142 <expand macro="column_metadata" dataset_name="hMPXV" extra_columns="outbreak,lineage,"/>
143 <expand macro="column_metadata" dataset_name="hMPXV_B1" extra_columns="outbreak,lineage,"/>
144 </conditional>
134 </actions> 145 </actions>
135 </data> 146 </data>
136 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)"> 147 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
137 <filter>outputs and "report_json" in outputs</filter> 148 <filter>outputs and "report_json" in outputs</filter>
138 </data> 149 </data>
143 <filter>outputs and "output_fasta" in outputs</filter> 154 <filter>outputs and "output_fasta" in outputs</filter>
144 </data> 155 </data>
145 </outputs> 156 </outputs>
146 <tests> 157 <tests>
147 <test expect_num_outputs="1"> 158 <test expect_num_outputs="1">
148 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 159 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
149 <conditional name="db"> 160 <conditional name="db">
150 <param name="source" value="download" /> 161 <param name="source" value="download"/>
151 </conditional> 162 </conditional>
152 <param name="outputs" value="report_tsv" /> 163 <param name="outputs" value="report_tsv"/>
153 <param name="organism" value="sars-cov-2" /> 164 <param name="organism" value="sars-cov-2"/>
154 <output name="report_tsv"> 165 <output name="report_tsv">
155 <assert_contents> 166 <assert_contents>
156 <has_n_columns n="66" /> 167 <has_n_columns n="67"/>
157 <has_text text="20A" /> 168 <has_text text="20A"/>
158 </assert_contents> 169 </assert_contents>
159 </output> 170 </output>
160 </test> 171 </test>
161 <test expect_num_outputs="3"> 172 <test expect_num_outputs="3">
162 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 173 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
163 <conditional name="db"> 174 <conditional name="db">
164 <param name="source" value="download" /> 175 <param name="source" value="download"/>
165 </conditional> 176 </conditional>
166 <param name="outputs" value="report_tsv,report_json,output_tree" /> 177 <param name="outputs" value="report_tsv,report_json,output_tree"/>
167 <param name="organism" value="sars-cov-2" /> 178 <param name="organism" value="sars-cov-2"/>
168 <output name="report_tsv"> 179 <output name="report_tsv">
169 <assert_contents> 180 <assert_contents>
170 <has_n_columns n="66" /> 181 <has_n_columns n="67"/>
171 <has_text text="20A" /> 182 <has_text text="20A"/>
172 </assert_contents> 183 </assert_contents>
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"/>
173 </output> 185 </output>
174 <output name="report_json"> 186 <output name="report_json">
175 <assert_contents> 187 <assert_contents>
176 <has_text text='"pos": 240,' /> 188 <has_text text="&quot;pos&quot;: 240,"/>
177 </assert_contents> 189 </assert_contents>
178 </output> 190 </output>
179 <output name="output_tree"> 191 <output name="output_tree">
180 <assert_contents> 192 <assert_contents>
181 <has_text text='"title": "QC Status"' /> 193 <has_text text="&quot;title&quot;: &quot;QC Status&quot;"/>
182 </assert_contents> 194 </assert_contents>
183 </output> 195 </output>
184 </test> 196 </test>
185 <test expect_num_outputs="1"> 197 <test expect_num_outputs="1">
186 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 198 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
187 <conditional name="db"> 199 <conditional name="db">
188 <param name="source" value="download" /> 200 <param name="source" value="download"/>
189 </conditional> 201 </conditional>
190 <param name="outputs" value="report_tsv" /> 202 <param name="outputs" value="report_tsv"/>
191 <param name="organism" value="sars-cov-2" /> 203 <param name="organism" value="sars-cov-2"/>
192 <conditional name="adv"> 204 <conditional name="adv">
193 <param name="advanced_options" value="yes" /> 205 <param name="advanced_options" value="yes"/>
194 <param name="input_qc_config" value="strict_qc.json" ftype="json" /> 206 <param name="input_qc_config" value="strict_qc.json" ftype="json"/>
195 </conditional> 207 </conditional>
196 <output name="report_tsv"> 208 <output name="report_tsv">
197 <assert_contents> 209 <assert_contents>
198 <has_n_columns n="66" /> 210 <has_n_columns n="67"/>
199 <has_text text="mediocre" /> 211 <has_text text="mediocre"/>
200 </assert_contents> 212 </assert_contents>
201 </output> 213 </output>
202 </test> 214 </test>
203 <test expect_num_outputs="2"> 215 <test expect_num_outputs="2">
204 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 216 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/>
205 <conditional name="db"> 217 <conditional name="db">
206 <param name="source" value="download" /> 218 <param name="source" value="download"/>
207 </conditional> 219 </conditional>
208 <param name="outputs" value="report_tsv,output_fasta" /> 220 <param name="outputs" value="report_tsv,output_fasta"/>
209 <param name="organism" value="sars-cov-2" /> 221 <param name="organism" value="sars-cov-2"/>
210 <conditional name="adv"> 222 <conditional name="adv">
211 <param name="advanced_options" value="yes" /> 223 <param name="advanced_options" value="yes"/>
212 <param name="include_reference" value="true" /> 224 <param name="include_reference" value="true"/>
213 </conditional> 225 </conditional>
214 <output name="report_tsv"> 226 <output name="report_tsv">
215 <assert_contents> 227 <assert_contents>
216 <has_n_columns n="66" /> 228 <has_n_columns n="67"/>
217 <has_text text="mediocre" /> 229 <has_text text="mediocre"/>
218 </assert_contents> 230 </assert_contents>
219 </output> 231 </output>
220 <output name="output_fasta" value="output_alignment.fasta" ftype="fasta" /> 232 <output name="output_fasta" value="output_alignment.fasta" ftype="fasta"/>
221 </test> 233 </test>
222 <test expect_num_outputs="1"> 234 <test expect_num_outputs="1">
223 <param name="input_fasta" value="mpxv.fasta.gz" ftype="fasta.gz" /> 235 <param name="input_fasta" value="mpxv.fasta.gz" ftype="fasta.gz"/>
224 <conditional name="db"> 236 <conditional name="db">
225 <param name="source" value="download" /> 237 <param name="source" value="download"/>
226 </conditional> 238 </conditional>
227 <param name="outputs" value="report_tsv" /> 239 <param name="outputs" value="report_tsv"/>
228 <param name="organism" value="MPXV" /> 240 <param name="organism" value="MPXV"/>
229 <output name="report_tsv"> 241 <output name="report_tsv">
230 <assert_contents> 242 <assert_contents>
231 <has_n_columns n="67" /> 243 <has_n_columns n="68"/>
232 <has_text text="hMPXV-1" /> 244 <has_text text="hMPXV-1"/>
233 </assert_contents> 245 </assert_contents>
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"/>
234 </output> 247 </output>
235 </test> 248 </test>
236 </tests> 249 </tests>
237 <help><![CDATA[ 250 <help><![CDATA[
238 251
259 * An Auspice v2 tree file in JSON format 272 * An Auspice v2 tree file in JSON format
260 273
261 .. _Nextclade: https://github.com/nextstrain/nextclade 274 .. _Nextclade: https://github.com/nextstrain/nextclade
262 275
263 ]]></help> 276 ]]></help>
264 <expand macro="citations" /> 277 <expand macro="citations"/>
265 </tool> 278 </tool>