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comparison macros.xml @ 18:6f40b91cd1ac draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
author iuc
date Sat, 08 Oct 2022 20:02:02 +0000
parents ae29ea21e448
children
comparison
equal deleted inserted replaced
17:f09378dd39b0 18:6f40b91cd1ac
1 <macros> 1 <macros>
2 <!-- same version number is used for nextclade and nextalign releases, even though they are distinct tools --> 2 <!-- same version number is used for nextclade and nextalign releases, even though they are distinct tools -->
3 <token name="@TOOL_VERSION@">2.4.0</token> 3 <token name="@TOOL_VERSION@">2.7.0</token>
4 <xml name="citations"> 4 <xml name="citations">
5 <citations> 5 <citations>
6 <citation type="bibtex">@online{nextclade, 6 <citation type="bibtex">@online{nextclade,
7 title={nextclade}, 7 title={nextclade},
8 year = 2021, 8 year = 2021,
9 url = {https://github.com/nextstrain/nextclade}, 9 url = {https://github.com/nextstrain/nextclade},
10 urldate = {2021-03-26} 10 urldate = {2021-03-26}
11 } 11 }
12 </citation> 12 </citation>
13 <yield /> 13 <yield/>
14 </citations> 14 </citations>
15 </xml> 15 </xml>
16
17 <!-- 16 <!--
18 command 17 command
19 --> 18 -->
20 <token name="@REF_FASTA@"><![CDATA[ 19 <token name="@REF_FASTA@"><![CDATA[
21 #if $reference_source.reference_source_selector == 'history': 20 #if $reference_source.reference_source_selector == 'history':
22 ln -f -s '$reference_source.ref_file' reference.fa && 21 ln -f -s '$reference_source.ref_file' reference.fa &&
23 #else: 22 #else:
24 ln -f -s '$reference_source.ref_file.fields.path' reference.fa && 23 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
25 #end if 24 #end if
26 ]]></token> 25 ]]></token>
27
28 <token name="@QUERY_FASTA@"><![CDATA[ 26 <token name="@QUERY_FASTA@"><![CDATA[
29 #if $input_fasta.is_of_type('fasta.gz') 27 #if $input_fasta.is_of_type('fasta.gz')
30 #set $query = 'query.fa.gz' 28 #set $query = 'query.fa.gz'
31 #else 29 #else
32 #set $query = 'query.fa' 30 #set $query = 'query.fa'
34 ln -s '$input_fasta' $query && 32 ln -s '$input_fasta' $query &&
35 ]]></token> 33 ]]></token>
36 <!-- 34 <!--
37 inputs 35 inputs
38 --> 36 -->
39
40 <xml name="reference"> 37 <xml name="reference">
41 <conditional name="reference_source"> 38 <conditional name="reference_source">
42 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome"> 39 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
43 <option value="cached">Use a built-in genome</option> 40 <option value="cached">Use a built-in genome</option>
44 <option value="history">Use a genome from history</option> 41 <option value="history">Use a genome from history</option>
54 <when value="history"> 51 <when value="history">
55 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference"/> 52 <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference"/>
56 </when> 53 </when>
57 </conditional> 54 </conditional>
58 </xml> 55 </xml>
59
60 <!-- 56 <!--
61 help 57 help
62 --> 58 -->
63 <token name="@NEXTCLADE@"><![CDATA[ 59 <token name="@NEXTCLADE@"><![CDATA[
64 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. 60 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.
65 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. 61 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.
66 ]]></token> 62 ]]></token>
67 63 <xml name="column_metadata" tokens="dataset_name" token_extra_columns="">
64 <!-- the columns in use are dependent on the dataset (i.e. database) - and extra columns seem to always be added in the same place -->
65 <!-- note that the tool is assuming that the dataset columns remain static: this might be an incorrect assumption in the future -->
66 <when value="@DATASET_NAME@">
67 <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"/>
68 </when>
69 </xml>
68 </macros> 70 </macros>