Mercurial > repos > iuc > nextclade
changeset 4:b74b9a7b3e3b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9"
| author | iuc |
|---|---|
| date | Mon, 23 Aug 2021 12:26:05 +0000 |
| parents | 3b75d5285aff |
| children | 0c46b95d60c3 |
| files | nextclade.xml |
| diffstat | 1 files changed, 45 insertions(+), 24 deletions(-) [+] |
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--- a/nextclade.xml Mon Jun 07 12:39:36 2021 +0000 +++ b/nextclade.xml Mon Aug 23 12:26:05 2021 +0000 @@ -2,15 +2,45 @@ <description></description> <macros> <import>macros.xml</import> - <token name="@TOOL_VERSION@">0.14.4</token> + <token name="@TOOL_VERSION@">1.2.3</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <requirements> - <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement> + <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement> + <requirement type="package">coreutils</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + export DB_PATH="\$(dirname "\$(dirname "\$(which nextclade)")")/share/nextclade" && + ln -s "\$DB_PATH" 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" + #if $adv.input_qc_config + #set $input_qc_config = $adv.input_qc_config + #end if + #if $adv.input_root_seq + #set $input_root_seq = $adv.input_root_seq + #end if + #if $adv.input_tree + #set $input_tree = $adv.input_tree + #end if + #if $adv.input_gene_map + #set $input_gene_map = $adv.input_gene_map + #end if + #if $adv.input_pcr_primers + #set $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 $outputs and "report_tsv" in $outputs #if $include_header --output-tsv '$report_tsv' @@ -24,21 +54,10 @@ #if $outputs and "output_tree" in $outputs --output-tree '${output_tree}' #end if - #if str($adv.advanced_options) == "yes" - #if $adv.input_qc_config - --input-qc-config '${adv.input_qc_config}' - #end if - #if $adv.input_root_seq - --input-root-seq '${adv.input_root_seq}' - #end if - #if $adv.input_tree - --input-tree '${adv.input_tree}' - #end if - #if $adv.input_gene_map - --input-gene-map '${adv.input_gene_map}' - #end if - #if $adv.input_pcr_primers - --input-pcr-primers '${adv.input_pcr_primers}' + #if $outputs and "output_fasta" in $outputs + --output-fasta "${output_fasta}" + #if str($adv.advanced_options) == "yes" + $adv.include_reference #end if #end if #if $outputs and "report_tsv" in $outputs and not $include_header @@ -51,6 +70,7 @@ <option value="report_json">JSON format report</option> <option value="report_tsv" selected="true">Tabular format report</option> <option value="output_tree">Auspice v2 tree file (JSON format)</option> + <option value="output_fasta">Aligned sequences (FASTA format)</option> </param> <param name="include_header" type="boolean" label="Include header line in output file" truevalue="true" falsevalue="false" /> @@ -65,6 +85,7 @@ <param argument="--input-tree" name="input_tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" /> <param argument="--input-gene-map" name="input_gene_map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing custom gene map. Gene map (sometimes also called 'gene annotations') is used to resolve aminoacid changes in genes" /> <param argument="--input-pcr-primers" name="input_pcr_primers" type="data" label="Custom PCR primer sites" format="json" optional="true" help="CSV file containing a list of custom PCR primer sites. These are used to report mutations in these sites" /> + <param argument="--include-reference" name="include_reference" type="boolean" label="Include reference sequence in FASTA alignment output" help="The FASTA alignment is an optional output of nextclade. Select this option to include the reference sequence in that alignment file" /> </when> <when value="no"> </when> @@ -74,10 +95,7 @@ <data name="report_tsv" format="tabular" label="${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,totalGaps,totalInsertions,totalMissing,totalMutations,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,missing,nonACGTNs,pcrPrimerChanges,aaSubstitutions,totalAminoacidSubstitutions,aaDeletions,totalAminoacidDeletions,alignmentEnd,alignmentScore,alignmentStart,qc.missingData.miss - ingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSit - es.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clus - teredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,errors" /> + <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalAminoacidSubstitutions,totalAminoacidDeletions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,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.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 ${on_string} (JSON report)"> @@ -86,6 +104,9 @@ <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)"> <filter>outputs and "output_tree" in outputs</filter> </data> + <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA alignment)"> + <filter>outputs and "output_fasta" in outputs</filter> + </data> </outputs> <tests> <test expect_num_outputs="1"> @@ -93,7 +114,7 @@ <param name="outputs" value="report_tsv" /> <output name="report_tsv"> <assert_contents> - <has_n_columns n="41" /> + <has_n_columns n="48" /> <has_text text="20A" /> </assert_contents> </output> @@ -103,7 +124,7 @@ <param name="outputs" value="report_tsv,report_json,output_tree" /> <output name="report_tsv"> <assert_contents> - <has_n_columns n="41" /> + <has_n_columns n="48" /> <has_text text="20A" /> </assert_contents> </output> @@ -127,7 +148,7 @@ </conditional> <output name="report_tsv"> <assert_contents> - <has_n_columns n="41" /> + <has_n_columns n="48" /> <has_text text="mediocre" /> </assert_contents> </output>