Mercurial > repos > iuc > nextclade
diff nextclade.xml @ 19:128ba8da994f draft
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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--- a/nextclade.xml Wed Aug 31 16:40:29 2022 +0000 +++ b/nextclade.xml Sat Oct 08 20:03:50 2022 +0000 @@ -68,18 +68,19 @@ #end if ]]></command> <inputs> - <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences" /> + <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences"/> <param name="organism" type="select" label="Organism"> <option value="sars-cov-2" selected="true">SARS-CoV-2</option> <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option> + <option value="sars-cov-2-21L">SARS-CoV-2 relative to BA.2</option> <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option> <option value="flu_h3n2_ha">Influenza A H3N2 HA</option> <option value="flu_vic_ha">Influenza B Victoria HA</option> <option value="flu_yam_ha">Influenza B Yamagata HA</option> - <option value="MPXV">Monkeypox (All Clades)</option> + <option value="MPXV">Monkeypox (All Clades - MPXV)</option> <option value="hMPXV">Human Monkeypox (hMPXV)</option> - <option value="hMPXV_B1">Human Monkeypox Clade B.1</option> - </param> + <option value="hMPXV_B1">Human Monkeypox Clade B.1 (hMPXV_B1)</option> + </param> <conditional name="db"> <param name="source" type="select" label="Version of database to use"> <option value="cached" selected="true">Use specific database version cached on this Galaxy server</option> @@ -88,17 +89,17 @@ <when value="cached"> <param name="release" label="Cached nextclade database release" type="select"> <options from_data_table="nextclade"> - <column name="value" index="0" /> - <column name="description" index="2" /> - <column name="date" index="4" /> - <column name="path" index="5" /> - <filter type="sort_by" column="4" /> - <filter type="param_value" ref="organism" column="1" /> - <filter type="regexp" column="3" value="@COMPATIBILITY_SPEC@" /> + <column name="value" index="0"/> + <column name="description" index="2"/> + <column name="date" index="4"/> + <column name="path" index="5"/> + <filter type="sort_by" column="4"/> + <filter type="param_value" ref="organism" column="1"/> + <filter type="regexp" column="3" value="@COMPATIBILITY_SPEC@"/> </options> </param> </when> - <when value="download"></when> + <when value="download"/> </conditional> <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true"> <option value="report_json">JSON format report</option> @@ -106,31 +107,41 @@ <option value="output_tree">Auspice v2 tree file (JSON format)</option> <option value="output_fasta">Aligned sequences (FASTA format)</option> </param> - <param name="include_header" type="boolean" label="Include header line in output file" - truevalue="true" falsevalue="false" /> + <param name="include_header" type="boolean" label="Include header line in output file" truevalue="true" falsevalue="false"/> <conditional name="adv"> - <param name="advanced_options" type="select" label="Use advanced options" > + <param name="advanced_options" type="select" label="Use advanced options"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> - <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" /> - <param argument="--input-root-seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence" /> - <param argument="--input-tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" /> - <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" /> - <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" /> - <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." /> - <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" /> + <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"/> + <param argument="--input-root-seq" type="data" label="Custom root sequence" format="txt" optional="true" help="Text file containing custom root sequence"/> + <param argument="--input-tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree"/> + <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"/> + <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"/> + <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."/> + <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"/> </when> <when value="no"> </when> </conditional> </inputs> <outputs> - <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)"> + <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)"> <filter>outputs and "report_tsv" in outputs</filter> <actions> - <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" /> + <conditional name="organism"> + <expand macro="column_metadata" dataset_name="sars-cov-2" extra_columns="Nextclade_pango,"/> + <expand macro="column_metadata" dataset_name="sars-cov-2-no-recomb" extra_columns="Nextclade_pango,"/> + <expand macro="column_metadata" dataset_name="sars-cov-2-21L" extra_columns="Nextclade_pango,partiallyAliased,immune_escape,ace2_binding,"/> + <expand macro="column_metadata" dataset_name="flu_h1n1pdm_ha"/> + <expand macro="column_metadata" dataset_name="flu_h3n2_ha"/> + <expand macro="column_metadata" dataset_name="flu_vic_ha"/> + <expand macro="column_metadata" dataset_name="flu_yam_ha"/> + <expand macro="column_metadata" dataset_name="MPXV" extra_columns="outbreak,lineage,"/> + <expand macro="column_metadata" dataset_name="hMPXV" extra_columns="outbreak,lineage,"/> + <expand macro="column_metadata" dataset_name="hMPXV_B1" extra_columns="outbreak,lineage,"/> + </conditional> </actions> </data> <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)"> @@ -145,92 +156,94 @@ </outputs> <tests> <test expect_num_outputs="1"> - <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> + <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/> <conditional name="db"> - <param name="source" value="download" /> + <param name="source" value="download"/> </conditional> - <param name="outputs" value="report_tsv" /> - <param name="organism" value="sars-cov-2" /> + <param name="outputs" value="report_tsv"/> + <param name="organism" value="sars-cov-2"/> <output name="report_tsv"> <assert_contents> - <has_n_columns n="66" /> - <has_text text="20A" /> + <has_n_columns n="67"/> + <has_text text="20A"/> </assert_contents> </output> </test> <test expect_num_outputs="3"> - <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> + <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/> <conditional name="db"> - <param name="source" value="download" /> + <param name="source" value="download"/> </conditional> - <param name="outputs" value="report_tsv,report_json,output_tree" /> - <param name="organism" value="sars-cov-2" /> + <param name="outputs" value="report_tsv,report_json,output_tree"/> + <param name="organism" value="sars-cov-2"/> <output name="report_tsv"> <assert_contents> - <has_n_columns n="66" /> - <has_text text="20A" /> + <has_n_columns n="67"/> + <has_text text="20A"/> </assert_contents> + <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"/> </output> <output name="report_json"> <assert_contents> - <has_text text='"pos": 240,' /> + <has_text text=""pos": 240,"/> </assert_contents> </output> <output name="output_tree"> <assert_contents> - <has_text text='"title": "QC Status"' /> + <has_text text=""title": "QC Status""/> </assert_contents> </output> </test> <test expect_num_outputs="1"> - <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> + <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/> <conditional name="db"> - <param name="source" value="download" /> + <param name="source" value="download"/> </conditional> - <param name="outputs" value="report_tsv" /> - <param name="organism" value="sars-cov-2" /> + <param name="outputs" value="report_tsv"/> + <param name="organism" value="sars-cov-2"/> <conditional name="adv"> - <param name="advanced_options" value="yes" /> - <param name="input_qc_config" value="strict_qc.json" ftype="json" /> + <param name="advanced_options" value="yes"/> + <param name="input_qc_config" value="strict_qc.json" ftype="json"/> </conditional> <output name="report_tsv"> <assert_contents> - <has_n_columns n="66" /> - <has_text text="mediocre" /> + <has_n_columns n="67"/> + <has_text text="mediocre"/> </assert_contents> </output> </test> <test expect_num_outputs="2"> - <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> + <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta"/> <conditional name="db"> - <param name="source" value="download" /> + <param name="source" value="download"/> </conditional> - <param name="outputs" value="report_tsv,output_fasta" /> - <param name="organism" value="sars-cov-2" /> + <param name="outputs" value="report_tsv,output_fasta"/> + <param name="organism" value="sars-cov-2"/> <conditional name="adv"> - <param name="advanced_options" value="yes" /> - <param name="include_reference" value="true" /> + <param name="advanced_options" value="yes"/> + <param name="include_reference" value="true"/> </conditional> <output name="report_tsv"> <assert_contents> - <has_n_columns n="66" /> - <has_text text="mediocre" /> + <has_n_columns n="67"/> + <has_text text="mediocre"/> </assert_contents> </output> - <output name="output_fasta" value="output_alignment.fasta" ftype="fasta" /> + <output name="output_fasta" value="output_alignment.fasta" ftype="fasta"/> </test> <test expect_num_outputs="1"> - <param name="input_fasta" value="mpxv.fasta.gz" ftype="fasta.gz" /> + <param name="input_fasta" value="mpxv.fasta.gz" ftype="fasta.gz"/> <conditional name="db"> - <param name="source" value="download" /> + <param name="source" value="download"/> </conditional> - <param name="outputs" value="report_tsv" /> - <param name="organism" value="MPXV" /> + <param name="outputs" value="report_tsv"/> + <param name="organism" value="MPXV"/> <output name="report_tsv"> <assert_contents> - <has_n_columns n="67" /> - <has_text text="hMPXV-1" /> + <has_n_columns n="68"/> + <has_text text="hMPXV-1"/> </assert_contents> + <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"/> </output> </test> </tests> @@ -261,5 +274,5 @@ .. _Nextclade: https://github.com/nextstrain/nextclade ]]></help> - <expand macro="citations" /> + <expand macro="citations"/> </tool>