Mercurial > repos > iuc > dada2_dada

annotate macros.xml.orig @ 5:e55eb3d22f79 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 07:56:53 +0000
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5
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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1 <?xml version="1.0"?>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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2 <macros>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <xml name="requirements">
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <requirements>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 <requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 <yield/>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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7 </requirements>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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8 </xml>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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9 <<<<<<< HEAD
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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10
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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11 <token name="@DADA2_VERSION@">1.20</token>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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12 =======
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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13 <xml name="bio_tools">
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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14 <xrefs>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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15 <xref type='bio.tools'>dada2</xref>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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16 </xrefs>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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17 </xml>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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18 <token name="@DADA2_VERSION@">1.16</token>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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19 >>>>>>> 449abf790 (add bio.tools ID)
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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20 <token name="@WRAPPER_VERSION@">0</token>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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21
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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22 <xml name="version_command">
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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23 <version_command><![CDATA[
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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24 echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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25 ]]></version_command>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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26 </xml>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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27
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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28 <xml name="stdio">
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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29 <stdio>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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30 <regex match="Error: cannot allocate" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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31 <regex match="'Calloc' could not allocate memory" source="stderr" level="fatal_oom" description="Out of memory error occurred" />
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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32 </stdio>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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33 </xml>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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34
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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35 <xml name="citations">
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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36 <citations>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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37 <citation type="doi">10.1038/nmeth.3869</citation>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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38 <yield/>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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39 </citations>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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40 </xml>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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41
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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42 <token name="@DADA_UNIQUES@">dada2_dada,dada2_mergepairs</token>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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43
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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44 <!-- function to read dada2 data types
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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45 - dada, and mergepairs are simply read as RDS
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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46 - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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47 - uniques is a named integer vector (columns=ASVs, only one rows)-->
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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48 <token name="@READ_FOO@"><![CDATA[
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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49 read.uniques <- function ( fname ) {
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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50 p <- read.table(fname, header=F, sep="\t")
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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51 n <-x[,2]
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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52 names(n)<-x[,1]
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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53 }
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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54 #def read_data($dataset)
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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55 #if $dataset.is_of_type('dada2_sequencetable')
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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56 t(as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) ))
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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57 #else if $dataset.is_of_type('dada2_uniques')
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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58 read.uniques('$dataset')
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59 #else if $dataset.is_of_type('tabular')
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60 read.table('$dataset', header=T, sep="\t", row.names=1)
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61 #else
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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62 readRDS('$dataset')
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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63 #end if
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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64 #end def
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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65 ]]></token>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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66 <!-- function to write dada2 data types (the content or the R variable 'out' is written)
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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67 - dada, and mergepairs are written as RDS
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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68 - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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69 - uniques is a named integer vector (columns=ASVs, only one rows)-->
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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70 <token name="@WRITE_FOO@"><![CDATA[
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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71 write.data <- function( data, fname, type ){
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72 if( type == 'dada2_uniques'){
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73 write.table(data, file = fname, quote = F, sep = "\t", row.names = T, col.names = F)
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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74 }else if( type== 'dada2_sequencetable'){
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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75 write.table(t(data), file=fname, quote=F, sep="\t", row.names = T, col.names = NA)
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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76 }else{
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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77 saveRDS(data, file=fname)
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78 }
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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79 }
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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80 ]]></token>
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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81
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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82 <xml name="fastq_input" token_multiple="" token_collection_type="" token_argument_fwd="" token_argument_rev="">
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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83 <conditional name="paired_cond">
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84 <param name="paired_select" type="select" label="Paired reads">
e55eb3d22f79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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85 <option value="paired">paired - in a data set pair</option>
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86 <option value="separate">paired - in two separate data sets</option>
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87 <option value="single">single</option>
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88 </param>
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89 <when value="paired">
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90 <param name="reads" argument="@ARGUMENT_FWD@/@ARGUMENT_REV@" type="data_collection" collection_type="@COLLECTION_TYPE@" format="fastq,fastq.gz" label="Paired short read data"/>
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91 </when>
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92 <when value="separate">
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93 <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Forward read data"/>
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94 <param name="sdaer" argument="@ARGUMENT_REV@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Reverse read data"/>
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95 </when>
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96 <when value="single">
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97 <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Short read data"/>
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98 </when>
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99 </conditional>
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100 </xml>
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101
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102 <!-- for filterAndTrim -->
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103 <xml name="trimmers">
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104 <section name="trim" title="Trimming parameters">
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105 <param argument="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/>
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106 <param argument="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/>
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107 <param argument="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/>
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108 <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded. (default 0: no truncation)"/>
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109 </section>
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110 </xml>
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111 <xml name="filters">
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112 <section name="filter" title="Filtering parameters">
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113 <param argument="maxLen" type="integer" value="" optional="true" min="0" label="Remove long reads" help="Remove reads with length greater than this value. Default: no length threshold"/>
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114 <param argument="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/>
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115 <param argument="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help="Note that some of the subsequent dada pipeline steps do not allow Ns"/>
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116 <param argument="minQ" type="integer" value="0" min="0" label="Remove low quality reads" help="Reads contain a quality score less than this value will be discarded"/>
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117 <param argument="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by number expected errors" help="Reads with a higher number of expected errors (EE) will be discarded, where EE = sum(10^(-Q_i/10)), with Q are the nominal quality scores at the read positions"/>
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118 </section>
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119 </xml>
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120
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121 <xml name="errorEstimationFunction">
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122 <param name="errfoo" argument="errorEstimationFunction" type="select" label="Error function">
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123 <option value="loessErrfun">loess: Use a loess fit to estimate error rates from transition counts</option>
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124 <option value="noqualErrfun">noqual: Estimate error rates for each type of transition while ignoring quality scores.</option>
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125 <option value="PacBioErrfun">PacBio: Estimate error rates from transition counts in PacBio CCS data.</option>
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126 </param>
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127 </xml>
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128 <token name="@HELP_OVERVIEW@"><![CDATA[
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129 Overview
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130 ........
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131
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132 The intended use of the dada2 tools for paired sequencing data is shown in the following image.
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133
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134 .. image:: pairpipe.png
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135
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136 Note: In particular for the analysis of paired collections the collections should be sorted lexicographical
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137 before the analysis.
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138
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139 For single end data you the steps "Unzip collection" and "mergePairs" are not necessary.
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140
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141 More information may be found on the dada2 homepage:: https://benjjneb.github.io/dada2/index.html (in particular tutorials) or the documentation of dada2's R package https://bioconductor.org/packages/release/bioc/html/dada2.html (in particular the pdf which contains the full documentation of all parameters)
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142 ]]></token>
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143 </macros>