| Previous changeset 18:feb40665d7cd (2022-08-31) Next changeset 20:4f6349228462 (2024-03-14) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8 |
|
modified:
macros.xml nextclade.xml |
| b |
| diff -r feb40665d7cd -r 128ba8da994f macros.xml --- a/macros.xml Wed Aug 31 16:40:29 2022 +0000 +++ b/macros.xml Sat Oct 08 20:03:50 2022 +0000 |
| [ |
| @@ -1,6 +1,6 @@ <macros> <!-- same version number is used for nextclade and nextalign releases, even though they are distinct tools --> - <token name="@TOOL_VERSION@">2.4.0</token> + <token name="@TOOL_VERSION@">2.7.0</token> <xml name="citations"> <citations> <citation type="bibtex">@online{nextclade, @@ -10,10 +10,9 @@ urldate = {2021-03-26} } </citation> - <yield /> + <yield/> </citations> </xml> - <!-- command --> @@ -24,7 +23,6 @@ ln -f -s '$reference_source.ref_file.fields.path' reference.fa && #end if ]]></token> - <token name="@QUERY_FASTA@"><![CDATA[ #if $input_fasta.is_of_type('fasta.gz') #set $query = 'query.fa.gz' @@ -36,7 +34,6 @@ <!-- inputs --> - <xml name="reference"> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> @@ -56,7 +53,6 @@ </when> </conditional> </xml> - <!-- help --> @@ -64,5 +60,11 @@ Nextclade is a tool that identifies differences between your sequences and a reference sequence, uses these differences to assign your sequences to clades, and reports potential sequence quality issues in your data. You can use the tool to analyze sequences before you upload them to a database, or if you want to assign Nextstrain clades to a set of sequences. ]]></token> - + <xml name="column_metadata" tokens="dataset_name" token_extra_columns=""> + <!-- the columns in use are dependent on the dataset (i.e. database) - and extra columns seem to always be added in the same place --> + <!-- note that the tool is assuming that the dataset columns remain static: this might be an incorrect assumption in the future --> + <when value="@DATASET_NAME@"> + <action name="column_names" type="metadata" default="seqName,clade,@EXTRA_COLUMNS@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"/> + </when> + </xml> </macros> |
| b |
| diff -r feb40665d7cd -r 128ba8da994f nextclade.xml --- a/nextclade.xml Wed Aug 31 16:40:29 2022 +0000 +++ b/nextclade.xml Sat Oct 08 20:03:50 2022 +0000 |
| b |
| b'@@ -68,18 +68,19 @@\n #end if \n ]]></command>\n <inputs>\n- <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences" />\n+ <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="FASTA file with input sequences"/>\n <param name="organism" type="select" label="Organism">\n <option value="sars-cov-2" selected="true">SARS-CoV-2</option>\n <option value="sars-cov-2-no-recomb">SARS-CoV-2 without recombinants</option>\n+ <option value="sars-cov-2-21L">SARS-CoV-2 relative to BA.2</option>\n <option value="flu_h1n1pdm_ha">Influenza A H1N1pdm HA</option>\n <option value="flu_h3n2_ha">Influenza A H3N2 HA</option>\n <option value="flu_vic_ha">Influenza B Victoria HA</option>\n <option value="flu_yam_ha">Influenza B Yamagata HA</option>\n- <option value="MPXV">Monkeypox (All Clades)</option>\n+ <option value="MPXV">Monkeypox (All Clades - MPXV)</option>\n <option value="hMPXV">Human Monkeypox (hMPXV)</option>\n- <option value="hMPXV_B1">Human Monkeypox Clade B.1</option>\n- </param> \n+ <option value="hMPXV_B1">Human Monkeypox Clade B.1 (hMPXV_B1)</option>\n+ </param>\n <conditional name="db">\n <param name="source" type="select" label="Version of database to use">\n <option value="cached" selected="true">Use specific database version cached on this Galaxy server</option>\n@@ -88,17 +89,17 @@\n <when value="cached">\n <param name="release" label="Cached nextclade database release" type="select">\n <options from_data_table="nextclade">\n- <column name="value" index="0" />\n- <column name="description" index="2" />\n- <column name="date" index="4" />\n- <column name="path" index="5" />\n- <filter type="sort_by" column="4" />\n- <filter type="param_value" ref="organism" column="1" />\n- <filter type="regexp" column="3" value="@COMPATIBILITY_SPEC@" />\n+ <column name="value" index="0"/>\n+ <column name="description" index="2"/>\n+ <column name="date" index="4"/>\n+ <column name="path" index="5"/>\n+ <filter type="sort_by" column="4"/>\n+ <filter type="param_value" ref="organism" column="1"/>\n+ <filter type="regexp" column="3" value="@COMPATIBILITY_SPEC@"/>\n </options>\n </param>\n </when>\n- <when value="download"></when>\n+ <when value="download"/>\n </conditional>\n <param name="outputs" type="select" label="Output options" help="Output reports and optionally tree" multiple="true">\n <option value="report_json">JSON format report</option>\n@@ -106,31 +107,41 @@\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+ <param name="include_header" type="boolean" label="Include header line in output file" truevalue="true" falsevalue="false"/>\n <conditional name="adv">\n- <param name="advanced_options" type="select" label="Use advanced options" >\n+ <param name="advanced_options" type="select" label="Use advanced options">\n <option value="yes">Yes</option>\n <option value="no" selected="true">No</option>\n </param>\n <when value="yes">\n- <param argument="--inpu'..b' value="sarscov2_1.fasta" ftype="fasta"/>\n <conditional name="db">\n- <param name="source" value="download" />\n+ <param name="source" value="download"/>\n </conditional>\n- <param name="outputs" value="report_tsv,output_fasta" />\n- <param name="organism" value="sars-cov-2" />\n+ <param name="outputs" value="report_tsv,output_fasta"/>\n+ <param name="organism" value="sars-cov-2"/>\n <conditional name="adv">\n- <param name="advanced_options" value="yes" />\n- <param name="include_reference" value="true" />\n+ <param name="advanced_options" value="yes"/>\n+ <param name="include_reference" value="true"/>\n </conditional>\n <output name="report_tsv">\n <assert_contents>\n- <has_n_columns n="66" />\n- <has_text text="mediocre" />\n+ <has_n_columns n="67"/>\n+ <has_text text="mediocre"/>\n </assert_contents>\n </output>\n- <output name="output_fasta" value="output_alignment.fasta" ftype="fasta" />\n+ <output name="output_fasta" value="output_alignment.fasta" ftype="fasta"/>\n </test>\n <test expect_num_outputs="1">\n- <param name="input_fasta" value="mpxv.fasta.gz" ftype="fasta.gz" />\n+ <param name="input_fasta" value="mpxv.fasta.gz" ftype="fasta.gz"/>\n <conditional name="db">\n- <param name="source" value="download" />\n+ <param name="source" value="download"/>\n </conditional>\n- <param name="outputs" value="report_tsv" />\n- <param name="organism" value="MPXV" />\n+ <param name="outputs" value="report_tsv"/>\n+ <param name="organism" value="MPXV"/>\n <output name="report_tsv">\n <assert_contents>\n- <has_n_columns n="67" />\n- <has_text text="hMPXV-1" />\n+ <has_n_columns n="68"/>\n+ <has_text text="hMPXV-1"/>\n </assert_contents>\n+ <metadata name="column_names" value="seqName,clade,outbreak,lineage,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"/>\n </output>\n </test>\n </tests>\n@@ -261,5 +274,5 @@\n .. _Nextclade: https://github.com/nextstrain/nextclade\n \n ]]></help>\n- <expand macro="citations" />\n+ <expand macro="citations"/>\n </tool>\n' |