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annotate macros.xml @ 15:41102a84e387 draft

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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 20:03:17 +0000
parents 4d93e708218c
children aadc5d8099e2
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d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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1 <macros>
2
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2 <!-- same version number is used for nextclade and nextalign releases, even though they are distinct tools -->
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41102a84e387 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit c41319b6593caa0a11835f5e8bc48b1f1e316ff8
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3 <token name="@TOOL_VERSION@">2.7.0</token>
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4 <xml name="citations">
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5 <citations>
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6 <citation type="bibtex">@online{nextclade,
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7 title={nextclade},
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8 year = 2021,
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9 url = {https://github.com/nextstrain/nextclade},
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10 urldate = {2021-03-26}
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11 }
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12 </citation>
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13 <yield/>
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14 </citations>
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15 </xml>
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16 <!--
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17 command
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18 -->
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19 <token name="@REF_FASTA@"><![CDATA[
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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20 #if $reference_source.reference_source_selector == 'history':
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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21 ln -f -s '$reference_source.ref_file' reference.fa &&
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22 #else:
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23 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
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24 #end if
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25 ]]></token>
14
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26 <token name="@QUERY_FASTA@"><![CDATA[
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27 #if $input_fasta.is_of_type('fasta.gz')
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28 #set $query = 'query.fa.gz'
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29 #else
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30 #set $query = 'query.fa'
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31 #end if
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32 ln -s '$input_fasta' $query &&
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33 ]]></token>
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34 <!--
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35 inputs
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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36 -->
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37 <xml name="reference">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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38 <conditional name="reference_source">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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39 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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40 <option value="cached">Use a built-in genome</option>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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41 <option value="history">Use a genome from history</option>
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42 </param>
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43 <when value="cached">
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44 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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45 <options from_data_table="all_fasta">
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46 <filter type="sort_by" column="2"/>
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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47 </options>
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48 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
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49 </param>
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50 </when>
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51 <when value="history">
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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"/>
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53 </when>
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54 </conditional>
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55 </xml>
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56 <!--
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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57 help
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58 -->
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59 <token name="@NEXTCLADE@"><![CDATA[
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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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.
d1dd7d1b07f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 66df2726d24d9f37eaaa31fea967a0553cc5c3e6"
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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.
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62 ]]></token>
15
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63 <xml name="column_metadata" tokens="dataset_name" token_extra_columns="">
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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 -->
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65 <!-- note that the tool is assuming that the dataset columns remain static: this might be an incorrect assumption in the future -->
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66 <when value="@DATASET_NAME@">
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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"/>
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68 </when>
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69 </xml>
4
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70 </macros>