Mercurial > repos > iuc > nextclade

comparison nextclade.xml @ 7:f6db3ce6ed1c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c033be45890203e175aa92a26da0d1510f1d1472"
author iuc
date Fri, 01 Oct 2021 07:47:24 +0000
parents 1e0234b87809
children 56b1a13d9680
comparison
equal deleted inserted replaced
6:1e0234b87809 7:f6db3ce6ed1c
99 </inputs> 99 </inputs>
100 <outputs> 100 <outputs>
101 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)"> 101 <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)">
102 <filter>outputs and "report_tsv" in outputs</filter> 102 <filter>outputs and "report_tsv" in outputs</filter>
103 <actions> 103 <actions>
104 <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" /> 104 <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" />
105 </actions> 105 </actions>
106 </data> 106 </data>
107 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)"> 107 <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">
108 <filter>outputs and "report_json" in outputs</filter> 108 <filter>outputs and "report_json" in outputs</filter>
109 </data> 109 </data>
119 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 119 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
120 <param name="outputs" value="report_tsv" /> 120 <param name="outputs" value="report_tsv" />
121 <param name="organism" value="sars-cov-2" /> 121 <param name="organism" value="sars-cov-2" />
122 <output name="report_tsv"> 122 <output name="report_tsv">
123 <assert_contents> 123 <assert_contents>
124 <has_n_columns n="48" /> 124 <has_n_columns n="52" />
125 <has_text text="20A" /> 125 <has_text text="20A" />
126 </assert_contents> 126 </assert_contents>
127 </output> 127 </output>
128 </test> 128 </test>
129 <test expect_num_outputs="3"> 129 <test expect_num_outputs="3">
130 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 130 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
131 <param name="outputs" value="report_tsv,report_json,output_tree" /> 131 <param name="outputs" value="report_tsv,report_json,output_tree" />
132 <param name="organism" value="sars-cov-2" /> 132 <param name="organism" value="sars-cov-2" />
133 <output name="report_tsv"> 133 <output name="report_tsv">
134 <assert_contents> 134 <assert_contents>
135 <has_n_columns n="48" /> 135 <has_n_columns n="52" />
136 <has_text text="20A" /> 136 <has_text text="20A" />
137 </assert_contents> 137 </assert_contents>
138 </output> 138 </output>
139 <output name="report_json"> 139 <output name="report_json">
140 <assert_contents> 140 <assert_contents>
141 <has_text text='"pos": 240,' /> 141 <has_text text='"pos": 240,' />
142 </assert_contents> 142 </assert_contents>
143 </output> 143 </output>
144 <output name="output_tree"> 144 <output name="output_tree">
145 <assert_contents> 145 <assert_contents>
146 <has_text text='"build_url": "https://github.com/nextstrain/nextclade"' /> 146 <has_text text='"title": "QC Status"' />
147 </assert_contents> 147 </assert_contents>
148 </output> 148 </output>
149 </test> 149 </test>
150 <test expect_num_outputs="1"> 150 <test expect_num_outputs="1">
151 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" /> 151 <param name="input_fasta" value="sarscov2_1.fasta" ftype="fasta" />
155 <param name="advanced_options" value="yes" /> 155 <param name="advanced_options" value="yes" />
156 <param name="input_qc_config" value="strict_qc.json" ftype="json" /> 156 <param name="input_qc_config" value="strict_qc.json" ftype="json" />
157 </conditional> 157 </conditional>
158 <output name="report_tsv"> 158 <output name="report_tsv">
159 <assert_contents> 159 <assert_contents>
160 <has_n_columns n="48" /> 160 <has_n_columns n="52" />
161 <has_text text="mediocre" /> 161 <has_text text="mediocre" />
162 </assert_contents> 162 </assert_contents>
163 </output> 163 </output>
164 </test> 164 </test>
165 </tests> 165 </tests>