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comparison macros.xml @ 7:96336c6a2bb7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit c2f6071f729b74540354f4a9e7084c9ac468a135
author iuc
date Mon, 07 Aug 2023 01:36:34 +0000
parents 84fd33a60b35
children 2cfceb9f9b8e
comparison
equal deleted inserted replaced
6:84fd33a60b35 7:96336c6a2bb7
10 <xrefs> 10 <xrefs>
11 <xref type="bio.tools">dada2</xref> 11 <xref type="bio.tools">dada2</xref>
12 <xref type="bioconductor">dada2</xref> 12 <xref type="bioconductor">dada2</xref>
13 </xrefs> 13 </xrefs>
14 </xml> 14 </xml>
15 <token name="@DADA2_VERSION@">1.20</token> 15 <token name="@DADA2_VERSION@">1.28</token>
16 <token name="@WRAPPER_VERSION@">1</token> 16 <token name="@WRAPPER_VERSION@">0</token>
17 17
18 <xml name="version_command"> 18 <xml name="version_command">
19 <version_command><![CDATA[ 19 <version_command><![CDATA[
20 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: ") 20 echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
21 ]]></version_command> 21 ]]></version_command>
41 - dada, and mergepairs are simply read as RDS 41 - dada, and mergepairs are simply read as RDS
42 - sequence_table is a named integer matrix (rows=samples, columns=ASVs) 42 - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
43 - uniques is a named integer vector (columns=ASVs, only one rows)--> 43 - uniques is a named integer vector (columns=ASVs, only one rows)-->
44 <token name="@READ_FOO@"><![CDATA[ 44 <token name="@READ_FOO@"><![CDATA[
45 read.uniques <- function ( fname ) { 45 read.uniques <- function ( fname ) {
46 p <- read.table(fname, header=F, sep="\t") 46 x <- read.table(fname, header=F, sep="\t")
47 n <-x[,2] 47 n <-x[,2]
48 names(n)<-x[,1] 48 names(n)<-x[,1]
49 return(n)
49 } 50 }
50 #def read_data($dataset) 51 #def read_data($dataset)
51 #if $dataset.is_of_type('dada2_sequencetable') 52 #if $dataset.is_of_type('dada2_sequencetable')
52 t(as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) )) 53 t(read.table('$dataset', header=T, sep="\t", row.names=1, check.names=FALSE))
53 #else if $dataset.is_of_type('dada2_uniques') 54 #else if $dataset.is_of_type('dada2_uniques')
54 read.uniques('$dataset') 55 read.uniques('$dataset')
55 #else if $dataset.is_of_type('tabular') 56 #else if $dataset.is_of_type('tabular')
56 read.table('$dataset', header=T, sep="\t", row.names=1) 57 read.table('$dataset', header=T, sep="\t", row.names=1, check.names=FALSE)
57 #else 58 #else
58 readRDS('$dataset') 59 readRDS('$dataset')
59 #end if 60 #end if
60 #end def 61 #end def
61 ]]></token> 62 ]]></token>
95 </conditional> 96 </conditional>
96 </xml> 97 </xml>
97 98
98 <!-- for filterAndTrim --> 99 <!-- for filterAndTrim -->
99 <xml name="trimmers"> 100 <xml name="trimmers">
100 <section name="trim" title="Trimming parameters"> 101 <section name="trim" title="Trimming parameters" expanded="true">
101 <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"/> 102 <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"/>
102 <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."/> 103 <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."/>
103 <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"/> 104 <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"/>
104 <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)"/> 105 <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)"/>
105 </section> 106 </section>
106 </xml> 107 </xml>
107 <xml name="filters"> 108 <xml name="filters">
108 <section name="filter" title="Filtering parameters"> 109 <section name="filter" title="Filtering parameters" expanded="true">
109 <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"/> 110 <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"/>
110 <param argument="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/> 111 <param argument="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/>
111 <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"/> 112 <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"/>
112 <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"/> 113 <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"/>
113 <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"/> 114 <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"/>