Mercurial > repos > iuc > nextclade
diff nextclade.xml @ 13:64be7ff9b97b draft
"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 |
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--- a/nextclade.xml Mon Jan 17 08:48:13 2022 +0000 +++ b/nextclade.xml Thu Jan 27 14:04:45 2022 +0000 @@ -11,35 +11,29 @@ <version_command>nextclade --version-detailed</version_command> <command detect_errors="exit_code"><![CDATA[ nextclade dataset get -n '${organism}' -o db && - #set $input_qc_config = "db/qc.json" - #set $input_root_seq = "db/reference.fasta" - #set $input_tree = "db/tree.json" - #set $input_gene_map = "db/genemap.gff" - #set $input_pcr_primers = "db/primers.csv" - #if str($adv.advanced_options) == "yes" + nextclade run + --input-fasta '${input_fasta}' + --input-dataset db/ + #if $adv.advanced_options == 'yes' #if $adv.input_qc_config - #set $input_qc_config = $adv.input_qc_config + --input-qc-config '$adv.input_qc_config' #end if #if $adv.input_root_seq - #set $input_root_seq = $adv.input_root_seq + --input-root-seq '$adv.input_root_seq' #end if #if $adv.input_tree - #set $input_tree = $adv.input_tree + --input-tree '$adv.input_tree' #end if #if $adv.input_gene_map - #set $input_gene_map = $adv.input_gene_map + --input-gene-map '$adv.input_gene_map' #end if #if $adv.input_pcr_primers - #set $input_pcr_primers = $adv.input_pcr_primers + --input-pcr-primers '$adv.input_pcr_primers' #end if - #end if - nextclade - --input-fasta '${input_fasta}' - --input-qc-config '${input_qc_config}' - --input-root-seq '${input_root_seq}' - --input-tree '${input_tree}' - --input-gene-map '${input_gene_map}' - --input-pcr-primers '${input_pcr_primers}' + #if $adv.input_virus_properties + --input-virus-properties '$adv.input_virus_properties' + #end if + #end if #if $outputs and "report_tsv" in $outputs #if $include_header --output-tsv '$report_tsv' @@ -91,7 +85,8 @@ <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" /> <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" /> <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" /> - <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" /> + <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." /> + <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" /> </when> <when value="no"> </when> @@ -101,7 +96,7 @@ <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,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" /> + <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" /> </actions> </data> <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)"> @@ -121,7 +116,7 @@ <param name="organism" value="sars-cov-2" /> <output name="report_tsv"> <assert_contents> - <has_n_columns n="53" /> + <has_n_columns n="62" /> <has_text text="20A" /> </assert_contents> </output> @@ -132,7 +127,7 @@ <param name="organism" value="sars-cov-2" /> <output name="report_tsv"> <assert_contents> - <has_n_columns n="53" /> + <has_n_columns n="62" /> <has_text text="20A" /> </assert_contents> </output> @@ -157,11 +152,27 @@ </conditional> <output name="report_tsv"> <assert_contents> - <has_n_columns n="53" /> + <has_n_columns n="62" /> <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="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" /> + </conditional> + <output name="report_tsv"> + <assert_contents> + <has_n_columns n="62" /> + <has_text text="mediocre" /> + </assert_contents> + </output> + <output name="output_fasta" value="output_alignment.fasta" ftype="fasta" /> + </test> </tests> <help><![CDATA[ @@ -171,6 +182,8 @@ Nextclade_ assigns clades, calls mutations and performs sequence quality checks on SARS-CoV-2 genomes. +For a description of nextclade's configuration files, see the `nextclade documentation <https://docs.nextstrain.org/projects/nextclade/en/latest/index.html>`_. + **Input** Input is a FASTA file containing one or more SARS-CoV-2 consensus genomes.