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

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit bc6ba57599c6516bd728e7311ba0a53188622edf

19:128ba8da994f

             with nextclade 2+ but at time of writing this tool is for nextclade version 2,
             so the following regexp will select all databases known to be compatible with
             this tool and exclude any requiring a future nextclade version 3. -->
        <token name="@COMPATIBILITY_SPEC@"><![CDATA[(^1\..+$|^2\.[0-4](\..+)*$)]]></token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
        <requirement type="package" version="9.0">coreutils</requirement>
    </requirements>
    <version_command>nextclade --version-detailed</version_command>

            </conditional>
            <param name="outputs" value="report_tsv"/>
            <param name="organism" value="sars-cov-2"/>
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="67"/>
                    <has_text text="20A"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">

            </conditional>
            <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="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">

                <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="67"/>
                    <has_text text="mediocre"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">

                <param name="advanced_options" value="yes"/>
                <param name="include_reference" value="true"/>
            </conditional>
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="67"/>
                    <has_text text="mediocre"/>
                </assert_contents>
            </output>
            <output name="output_fasta" value="output_alignment.fasta" ftype="fasta"/>
        </test>

20:4f6349228462

             with nextclade 2+ but at time of writing this tool is for nextclade version 2,
             so the following regexp will select all databases known to be compatible with
             this tool and exclude any requiring a future nextclade version 3. -->
        <token name="@COMPATIBILITY_SPEC@"><![CDATA[(^1\..+$|^2\.[0-4](\..+)*$)]]></token>
    </macros>
    <expand macro="xrefs"/>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>
        <requirement type="package" version="9.0">coreutils</requirement>
    </requirements>
    <version_command>nextclade --version-detailed</version_command>

            </conditional>
            <param name="outputs" value="report_tsv"/>
            <param name="organism" value="sars-cov-2"/>
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="71"/>
                    <has_text text="20A"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">

            </conditional>
            <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="71"/>
                    <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">

                <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="71"/>
                    <has_text text="mediocre"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="2">

                <param name="advanced_options" value="yes"/>
                <param name="include_reference" value="true"/>
            </conditional>
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="71"/>
                    <has_text text="mediocre"/>
                </assert_contents>
            </output>
            <output name="output_fasta" value="output_alignment.fasta" ftype="fasta"/>
        </test>