Mercurial > repos > iuc > nextclade
changeset 1:495c19a62538 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 8a6f8a1c1cb3fea223e6bf628b930a1182088b0b"
| author | iuc |
|---|---|
| date | Thu, 20 May 2021 21:10:18 +0000 |
| parents | 919cc9dc23f0 |
| children | efbf471df058 |
| files | nextclade.xml |
| diffstat | 1 files changed, 22 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/nextclade.xml Mon Apr 26 19:08:26 2021 +0000 +++ b/nextclade.xml Thu May 20 21:10:18 2021 +0000 @@ -2,8 +2,8 @@ <description></description> <macros> <import>macros.xml</import> - <token name="@TOOL_VERSION@">0.14.2</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@TOOL_VERSION@">0.14.3</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement> @@ -12,7 +12,11 @@ nextclade --input-fasta '${input_fasta}' #if $outputs and "report_tsv" in $outputs - --output-tsv '${report_tsv}' + #if $include_header + --output-tsv '$report_tsv' + #else + --output-tsv report.tsv + #end if #end if #if $outputs and "report_json" in $outputs --output-json '${report_json}' @@ -37,6 +41,9 @@ --input-pcr-primers '${adv.input_pcr_primers}' #end if #end if + #if $outputs and "report_tsv" in $outputs and not $include_header + && tail -n+2 report.tsv >'$report_tsv' + #end if ]]></command> <inputs> <param argument="--input-fasta" name="input_fasta" type="data" format="fasta" label="SARS-CoV-2 consensus sequences (FASTA)" /> @@ -45,6 +52,8 @@ <option value="report_tsv" selected="true">Tabular format report</option> <option value="output_tree">Auspice v2 tree file (JSON format)</option> </param> + <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" > <option value="yes">Yes</option> @@ -62,8 +71,14 @@ </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 ${on_string} (TSV report)"> <filter>outputs and "report_tsv" in outputs</filter> + <actions> + <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalGaps,totalInsertions,totalMissing,totalMutations,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertionsmissing,nonACGTNs,pcrPrimerChanges,aaSubstitutions,totalAminoacidSubstitutions,aaDeletions,totalAminoacidDeletions,alignmentEnd,alignmentScore,alignmentStart,qc.missingData.miss + ingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSit + es.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clus + teredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,errors" /> + </actions> </data> <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)"> <filter>outputs and "report_json" in outputs</filter> @@ -78,6 +93,7 @@ <param name="outputs" value="report_tsv" /> <output name="report_tsv"> <assert_contents> + <has_n_columns n="41" /> <has_text text="20A" /> </assert_contents> </output> @@ -87,6 +103,7 @@ <param name="outputs" value="report_tsv,report_json,output_tree" /> <output name="report_tsv"> <assert_contents> + <has_n_columns n="41" /> <has_text text="20A" /> </assert_contents> </output> @@ -110,6 +127,7 @@ </conditional> <output name="report_tsv"> <assert_contents> + <has_n_columns n="41" /> <has_text text="mediocre" /> </assert_contents> </output>