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comparison nextclade.xml @ 20:4f6349228462 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit bc6ba57599c6516bd728e7311ba0a53188622edf
author iuc
date Thu, 14 Mar 2024 13:26:08 +0000
parents 128ba8da994f
children
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19:128ba8da994f 20:4f6349228462
7 with nextclade 2+ but at time of writing this tool is for nextclade version 2, 7 with nextclade 2+ but at time of writing this tool is for nextclade version 2,
8 so the following regexp will select all databases known to be compatible with 8 so the following regexp will select all databases known to be compatible with
9 this tool and exclude any requiring a future nextclade version 3. --> 9 this tool and exclude any requiring a future nextclade version 3. -->
10 <token name="@COMPATIBILITY_SPEC@"><![CDATA[(^1\..+$|^2\.[0-4](\..+)*$)]]></token> 10 <token name="@COMPATIBILITY_SPEC@"><![CDATA[(^1\..+$|^2\.[0-4](\..+)*$)]]></token>
11 </macros> 11 </macros>
12 <expand macro="xrefs"/>
12 <requirements> 13 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement> 14 <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
14 <requirement type="package" version="9.0">coreutils</requirement> 15 <requirement type="package" version="9.0">coreutils</requirement>
15 </requirements> 16 </requirements>
16 <version_command>nextclade --version-detailed</version_command> 17 <version_command>nextclade --version-detailed</version_command>
162 </conditional> 163 </conditional>
163 <param name="outputs" value="report_tsv"/> 164 <param name="outputs" value="report_tsv"/>
164 <param name="organism" value="sars-cov-2"/> 165 <param name="organism" value="sars-cov-2"/>
165 <output name="report_tsv"> 166 <output name="report_tsv">
166 <assert_contents> 167 <assert_contents>
167 <has_n_columns n="67"/> 168 <has_n_columns n="71"/>
168 <has_text text="20A"/> 169 <has_text text="20A"/>
169 </assert_contents> 170 </assert_contents>
170 </output> 171 </output>
171 </test> 172 </test>
172 <test expect_num_outputs="3"> 173 <test expect_num_outputs="3">
176 </conditional> 177 </conditional>
177 <param name="outputs" value="report_tsv,report_json,output_tree"/> 178 <param name="outputs" value="report_tsv,report_json,output_tree"/>
178 <param name="organism" value="sars-cov-2"/> 179 <param name="organism" value="sars-cov-2"/>
179 <output name="report_tsv"> 180 <output name="report_tsv">
180 <assert_contents> 181 <assert_contents>
181 <has_n_columns n="67"/> 182 <has_n_columns n="71"/>
182 <has_text text="20A"/> 183 <has_text text="20A"/>
183 </assert_contents> 184 </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"/> 185 <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"/>
185 </output> 186 </output>
186 <output name="report_json"> 187 <output name="report_json">
205 <param name="advanced_options" value="yes"/> 206 <param name="advanced_options" value="yes"/>
206 <param name="input_qc_config" value="strict_qc.json" ftype="json"/> 207 <param name="input_qc_config" value="strict_qc.json" ftype="json"/>
207 </conditional> 208 </conditional>
208 <output name="report_tsv"> 209 <output name="report_tsv">
209 <assert_contents> 210 <assert_contents>
210 <has_n_columns n="67"/> 211 <has_n_columns n="71"/>
211 <has_text text="mediocre"/> 212 <has_text text="mediocre"/>
212 </assert_contents> 213 </assert_contents>
213 </output> 214 </output>
214 </test> 215 </test>
215 <test expect_num_outputs="2"> 216 <test expect_num_outputs="2">
223 <param name="advanced_options" value="yes"/> 224 <param name="advanced_options" value="yes"/>
224 <param name="include_reference" value="true"/> 225 <param name="include_reference" value="true"/>
225 </conditional> 226 </conditional>
226 <output name="report_tsv"> 227 <output name="report_tsv">
227 <assert_contents> 228 <assert_contents>
228 <has_n_columns n="67"/> 229 <has_n_columns n="71"/>
229 <has_text text="mediocre"/> 230 <has_text text="mediocre"/>
230 </assert_contents> 231 </assert_contents>
231 </output> 232 </output>
232 <output name="output_fasta" value="output_alignment.fasta" ftype="fasta"/> 233 <output name="output_fasta" value="output_alignment.fasta" ftype="fasta"/>
233 </test> 234 </test>