comparison nextclade.xml @ 7:f6db3ce6ed1c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"

6:1e0234b87809

    </inputs>
    <outputs>
        <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">            
            <filter>outputs and "report_tsv" in outputs</filter>
            <actions>
                <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalAminoacidSubstitutions,totalAminoacidDeletions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,aaSubstitutions,aaDeletions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,errors" />                
            </actions>
        </data>
        <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
            <filter>outputs and "report_json" in outputs</filter>
        </data>

            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <param name="outputs" value="report_tsv" />
            <param name="organism" value="sars-cov-2" />
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="48" />
                    <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="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="48" />
                    <has_text text="20A" />
                </assert_contents>
            </output>
            <output name="report_json">
                <assert_contents>
                    <has_text text='"pos": 240,' />
                </assert_contents>
            </output>
            <output name="output_tree">
                <assert_contents>
                    <has_text text='"build_url": "https://github.com/nextstrain/nextclade"' />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />

                <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="48" />
                    <has_text text="mediocre" />
                </assert_contents>
            </output>
        </test>
    </tests>

7:f6db3ce6ed1c

    </inputs>
    <outputs>
        <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">            
            <filter>outputs and "report_tsv" in outputs</filter>
            <actions>
                <action name="column_names" type="metadata" default="seqName,clade,qc.overallScore,qc.overallStatus,totalSubstitutions,totalDeletions,totalInsertions,totalFrameShifts,totalAminoacidSubstitutions,totalAminoacidDeletions,totalMissing,totalNonACGTNs,totalPcrPrimerChanges,substitutions,deletions,insertions,frameShifts,aaSubstitutions,aaDeletions,missing,nonACGTNs,pcrPrimerChanges,alignmentScore,alignmentStart,alignmentEnd,qc.missingData.missingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSites.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clusteredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,qc.frameShifts.frameShifts,qc.frameShifts.totalFrameShifts,qc.frameShifts.frameShiftsIgnored,qc.frameShifts.totalFrameShiftsIgnored,qc.frameShifts.score,qc.frameShifts.status,qc.stopCodons.stopCodons,qc.stopCodons.totalStopCodons,qc.stopCodons.score,qc.stopCodons.status,errors" />
            </actions>
        </data>
        <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
            <filter>outputs and "report_json" in outputs</filter>
        </data>

            <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
            <param name="outputs" value="report_tsv" />
            <param name="organism" value="sars-cov-2" />
            <output name="report_tsv">
                <assert_contents>
                    <has_n_columns n="52" />
                    <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="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="52" />
                    <has_text text="20A" />
                </assert_contents>
            </output>
            <output name="report_json">
                <assert_contents>
                    <has_text text='"pos": 240,' />
                </assert_contents>
            </output>
            <output name="output_tree">
                <assert_contents>
                    <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="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="52" />
                    <has_text text="mediocre" />
                </assert_contents>
            </output>
        </test>
    </tests>