| Previous changeset 3:3b75d5285aff (2021-06-07) Next changeset 5:0c46b95d60c3 (2021-09-01) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit e6c24a9360cd88f87804b6e7648295d6f300eac9" |
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modified:
nextclade.xml |
| b |
| diff -r 3b75d5285aff -r b74b9a7b3e3b nextclade.xml --- a/nextclade.xml Mon Jun 07 12:39:36 2021 +0000 +++ b/nextclade.xml Mon Aug 23 12:26:05 2021 +0000 |
| [ |
| b'@@ -2,15 +2,45 @@\n <description></description>\n <macros>\n <import>macros.xml</import>\n- <token name="@TOOL_VERSION@">0.14.4</token>\n+ <token name="@TOOL_VERSION@">1.2.3</token>\n <token name="@VERSION_SUFFIX@">0</token>\n </macros>\n <requirements>\n- <requirement type="package" version="@TOOL_VERSION@">nextclade_js</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">nextclade</requirement>\n+ <requirement type="package">coreutils</requirement>\n </requirements>\n <command detect_errors="exit_code"><![CDATA[\n+ export DB_PATH="\\$(dirname "\\$(dirname "\\$(which nextclade)")")/share/nextclade" &&\n+ ln -s "\\$DB_PATH" db &&\n+ #set $input_qc_config = "db/qc.json"\n+ #set $input_root_seq = "db/reference.fasta"\n+ #set $input_tree = "db/tree.json"\n+ #set $input_gene_map = "db/genemap.gff"\n+ #set $input_pcr_primers = "db/primers.csv"\n+ #if str($adv.advanced_options) == "yes"\n+ #if $adv.input_qc_config\n+ #set $input_qc_config = $adv.input_qc_config\n+ #end if\n+ #if $adv.input_root_seq\n+ #set $input_root_seq = $adv.input_root_seq\n+ #end if\n+ #if $adv.input_tree\n+ #set $input_tree = $adv.input_tree\n+ #end if\n+ #if $adv.input_gene_map\n+ #set $input_gene_map = $adv.input_gene_map\n+ #end if \n+ #if $adv.input_pcr_primers\n+ #set $input_pcr_primers = $adv.input_pcr_primers\n+ #end if\n+ #end if \n nextclade\n --input-fasta \'${input_fasta}\'\n+ --input-qc-config \'${input_qc_config}\'\n+ --input-root-seq \'${input_root_seq}\'\n+ --input-tree \'${input_tree}\'\n+ --input-gene-map \'${input_gene_map}\'\n+ --input-pcr-primers \'${input_pcr_primers}\'\n #if $outputs and "report_tsv" in $outputs\n #if $include_header\n --output-tsv \'$report_tsv\'\n@@ -24,21 +54,10 @@\n #if $outputs and "output_tree" in $outputs\n --output-tree \'${output_tree}\'\n #end if\n- #if str($adv.advanced_options) == "yes"\n- #if $adv.input_qc_config\n- --input-qc-config \'${adv.input_qc_config}\'\n- #end if\n- #if $adv.input_root_seq\n- --input-root-seq \'${adv.input_root_seq}\'\n- #end if\n- #if $adv.input_tree\n- --input-tree \'${adv.input_tree}\'\n- #end if\n- #if $adv.input_gene_map\n- --input-gene-map \'${adv.input_gene_map}\'\n- #end if \n- #if $adv.input_pcr_primers\n- --input-pcr-primers \'${adv.input_pcr_primers}\'\n+ #if $outputs and "output_fasta" in $outputs\n+ --output-fasta "${output_fasta}"\n+ #if str($adv.advanced_options) == "yes"\n+ $adv.include_reference\n #end if\n #end if\n #if $outputs and "report_tsv" in $outputs and not $include_header\n@@ -51,6 +70,7 @@\n <option value="report_json">JSON format report</option>\n <option value="report_tsv" selected="true">Tabular format report</option>\n <option value="output_tree">Auspice v2 tree file (JSON format)</option>\n+ <option value="output_fasta">Aligned sequences (FASTA format)</option>\n </param>\n <param name="include_header" type="boolean" label="Include header line in output file" \n truevalue="true" falsevalue="false" /> \n@@ -65,6 +85,7 @@\n <param argument="--input-tree" name="input_tree" type="data" label="Custom reference tree" format="json" optional="true" help="Auspice JSON v2 file containing custom reference tree" />\n <param argument="--input-gene-map" name="input_gene_map" type="data" label="Custom gene map" format="json" optional="true" help="JSON file containing cust'..b'ude the reference sequence in that alignment file" /> \n </when>\n <when value="no">\n </when>\n@@ -74,10 +95,7 @@\n <data name="report_tsv" format="tabular" label="${tool.name} on ${on_string} (TSV report)"> \n <filter>outputs and "report_tsv" in outputs</filter>\n <actions>\n- <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\n- ingDataThreshold,qc.missingData.score,qc.missingData.status,qc.missingData.totalMissing,qc.mixedSites.mixedSitesThreshold,qc.mixedSites.score,qc.mixedSites.status,qc.mixedSit\n- es.totalMixedSites,qc.privateMutations.cutoff,qc.privateMutations.excess,qc.privateMutations.score,qc.privateMutations.status,qc.privateMutations.total,qc.snpClusters.clus\n- teredSNPs,qc.snpClusters.score,qc.snpClusters.status,qc.snpClusters.totalSNPs,errors" />\n+ <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" /> \n </actions>\n </data>\n <data name="report_json" format="json" label="${tool.name} on ${on_string} (JSON report)">\n@@ -86,6 +104,9 @@\n <data name="output_tree" format="json" label="${tool.name} on ${on_string} (Auspice v2 tree)">\n <filter>outputs and "output_tree" in outputs</filter>\n </data>\n+ <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA alignment)">\n+ <filter>outputs and "output_fasta" in outputs</filter>\n+ </data>\n </outputs>\n <tests>\n <test expect_num_outputs="1">\n@@ -93,7 +114,7 @@\n <param name="outputs" value="report_tsv" />\n <output name="report_tsv">\n <assert_contents>\n- <has_n_columns n="41" />\n+ <has_n_columns n="48" />\n <has_text text="20A" />\n </assert_contents>\n </output>\n@@ -103,7 +124,7 @@\n <param name="outputs" value="report_tsv,report_json,output_tree" />\n <output name="report_tsv">\n <assert_contents>\n- <has_n_columns n="41" />\n+ <has_n_columns n="48" />\n <has_text text="20A" />\n </assert_contents>\n </output>\n@@ -127,7 +148,7 @@\n </conditional>\n <output name="report_tsv">\n <assert_contents>\n- <has_n_columns n="41" />\n+ <has_n_columns n="48" />\n <has_text text="mediocre" />\n </assert_contents>\n </output>\n' |