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comparison macros.xml @ 9:d908015e5889 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit a54770771e567c7ad8a9dd75cc4689c3935ef11c
author matthias
date Tue, 28 May 2019 12:15:38 -0400
parents 7970dfbedde3
children 279014cdd101
comparison
equal deleted inserted replaced
8:7970dfbedde3 9:d908015e5889
24 </xml> 24 </xml>
25 25
26 <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token> 26 <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>
27 27
28 <!-- function to read dada2 data types 28 <!-- function to read dada2 data types
29 - derep, dada, and mergepairs are simply read as RDS 29 - derep, dada, and mergepairs are simply read as RDS
30 - sequence_table is a named integer matrix (rows=samples, columns=ASVs) 30 - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
31 - uniques is a named integer vector (columns=ASVs, only one rows)--> 31 - uniques is a named integer vector (columns=ASVs, only one rows)-->
32 <token name="@READ_FOO@"><![CDATA[ 32 <token name="@READ_FOO@"><![CDATA[
33 read.uniques <- function ( fname ) { 33 read.uniques <- function ( fname ) {
34 p <- read.table(fname, header=F, sep="\t") 34 p <- read.table(fname, header=F, sep="\t")
46 readRDS('$dataset') 46 readRDS('$dataset')
47 #end if 47 #end if
48 #end def 48 #end def
49 ]]></token> 49 ]]></token>
50 <!-- function to write dada2 data types (the content or the R variable 'out' is written) 50 <!-- function to write dada2 data types (the content or the R variable 'out' is written)
51 - derep, dada, and mergepairs are written as RDS 51 - derep, dada, and mergepairs are written as RDS
52 - sequence_table is a named integer matrix (rows=samples, columns=ASVs) 52 - sequence_table is a named integer matrix (rows=samples, columns=ASVs)
53 - uniques is a named integer vector (columns=ASVs, only one rows)--> 53 - uniques is a named integer vector (columns=ASVs, only one rows)-->
54 <token name="@WRITE_FOO@"><![CDATA[ 54 <token name="@WRITE_FOO@"><![CDATA[
55 write.data <- function( data, fname, type ){ 55 write.data <- function( data, fname, type ){
56 if( type == 'dada2_uniques'){ 56 if( type == 'dada2_uniques'){
59 write.table(t(data), file=fname, quote=F, sep="\t", row.names = T, col.names = NA) 59 write.table(t(data), file=fname, quote=F, sep="\t", row.names = T, col.names = NA)
60 }else{ 60 }else{
61 saveRDS(data, file=fname) 61 saveRDS(data, file=fname)
62 } 62 }
63 } 63 }
64 ]]></token> 64 ]]></token>
65
66 <xml name="fastq_input" token_multiple="" token_collection_type="" token_argument_fwd="" token_argument_rev="">
67 <conditional name="paired_cond">
68 <param name="paired_select" type="select" label="Paired reads">
69 <option value="paired">paired - in a data set pair</option>
70 <option value="separate">paired - in two separate data sets</option>
71 <option value="single">single</option>
72 </param>
73 <when value="paired">
74 <param name="reads" argument="@ARGUMENT_FWD@/@ARGUMENT_REV@" type="data_collection" collection_type="@COLLECTION_TYPE@" format="fastq,fastq.gz" label="Paired short read data"/>
75 </when>
76 <when value="separate">
77 <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Forward read data"/>
78 <param name="sdaer" argument="@ARGUMENT_REV@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Reverse read data"/>
79 </when>
80 <when value="single">
81 <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Short read data"/>
82 </when>
83 </conditional>
84 </xml>
65 85
66 <!-- for filterAndTrim --> 86 <!-- for filterAndTrim -->
67 <xml name="trimmers"> 87 <xml name="trimmers">
68 <section name="trim" title="Trimming parameters"> 88 <section name="trim" title="Trimming parameters">
69 <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"/> 89 <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"/>
70 <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."/> 90 <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."/>
71 <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"/> 91 <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"/>
72 <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)"/> 92 <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)"/>
73 </section> 93 </section>
74 </xml> 94 </xml>
75 <xml name="filters"> 95 <xml name="filters">
76 <section name="filter" title="Filtering parameters"> 96 <section name="filter" title="Filtering parameters">
77 <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"/> 97 <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"/>