Mercurial > repos > iuc > dada2_dada
comparison macros.xml.orig @ 5:e55eb3d22f79 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author | iuc |
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date | Tue, 31 Aug 2021 07:56:53 +0000 |
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4:21bd1282d216 | 5:e55eb3d22f79 |
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1 <?xml version="1.0"?> | |
2 <macros> | |
3 <xml name="requirements"> | |
4 <requirements> | |
5 <requirement type="package" version="@DADA2_VERSION@">bioconductor-dada2</requirement> | |
6 <yield/> | |
7 </requirements> | |
8 </xml> | |
9 <<<<<<< HEAD | |
10 | |
11 <token name="@DADA2_VERSION@">1.20</token> | |
12 ======= | |
13 <xml name="bio_tools"> | |
14 <xrefs> | |
15 <xref type='bio.tools'>dada2</xref> | |
16 </xrefs> | |
17 </xml> | |
18 <token name="@DADA2_VERSION@">1.16</token> | |
19 >>>>>>> 449abf790 (add bio.tools ID) | |
20 <token name="@WRAPPER_VERSION@">0</token> | |
21 | |
22 <xml name="version_command"> | |
23 <version_command><![CDATA[ | |
24 echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ") | |
25 ]]></version_command> | |
26 </xml> | |
27 | |
28 <xml name="stdio"> | |
29 <stdio> | |
30 <regex match="Error: cannot allocate" source="stderr" level="fatal_oom" description="Out of memory error occurred" /> | |
31 <regex match="'Calloc' could not allocate memory" source="stderr" level="fatal_oom" description="Out of memory error occurred" /> | |
32 </stdio> | |
33 </xml> | |
34 | |
35 <xml name="citations"> | |
36 <citations> | |
37 <citation type="doi">10.1038/nmeth.3869</citation> | |
38 <yield/> | |
39 </citations> | |
40 </xml> | |
41 | |
42 <token name="@DADA_UNIQUES@">dada2_dada,dada2_mergepairs</token> | |
43 | |
44 <!-- function to read dada2 data types | |
45 - dada, and mergepairs are simply read as RDS | |
46 - sequence_table is a named integer matrix (rows=samples, columns=ASVs) | |
47 - uniques is a named integer vector (columns=ASVs, only one rows)--> | |
48 <token name="@READ_FOO@"><![CDATA[ | |
49 read.uniques <- function ( fname ) { | |
50 p <- read.table(fname, header=F, sep="\t") | |
51 n <-x[,2] | |
52 names(n)<-x[,1] | |
53 } | |
54 #def read_data($dataset) | |
55 #if $dataset.is_of_type('dada2_sequencetable') | |
56 t(as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) )) | |
57 #else if $dataset.is_of_type('dada2_uniques') | |
58 read.uniques('$dataset') | |
59 #else if $dataset.is_of_type('tabular') | |
60 read.table('$dataset', header=T, sep="\t", row.names=1) | |
61 #else | |
62 readRDS('$dataset') | |
63 #end if | |
64 #end def | |
65 ]]></token> | |
66 <!-- function to write dada2 data types (the content or the R variable 'out' is written) | |
67 - dada, and mergepairs are written as RDS | |
68 - sequence_table is a named integer matrix (rows=samples, columns=ASVs) | |
69 - uniques is a named integer vector (columns=ASVs, only one rows)--> | |
70 <token name="@WRITE_FOO@"><![CDATA[ | |
71 write.data <- function( data, fname, type ){ | |
72 if( type == 'dada2_uniques'){ | |
73 write.table(data, file = fname, quote = F, sep = "\t", row.names = T, col.names = F) | |
74 }else if( type== 'dada2_sequencetable'){ | |
75 write.table(t(data), file=fname, quote=F, sep="\t", row.names = T, col.names = NA) | |
76 }else{ | |
77 saveRDS(data, file=fname) | |
78 } | |
79 } | |
80 ]]></token> | |
81 | |
82 <xml name="fastq_input" token_multiple="" token_collection_type="" token_argument_fwd="" token_argument_rev=""> | |
83 <conditional name="paired_cond"> | |
84 <param name="paired_select" type="select" label="Paired reads"> | |
85 <option value="paired">paired - in a data set pair</option> | |
86 <option value="separate">paired - in two separate data sets</option> | |
87 <option value="single">single</option> | |
88 </param> | |
89 <when value="paired"> | |
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"/> | |
91 </when> | |
92 <when value="separate"> | |
93 <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Forward read data"/> | |
94 <param name="sdaer" argument="@ARGUMENT_REV@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Reverse read data"/> | |
95 </when> | |
96 <when value="single"> | |
97 <param name="reads" argument="@ARGUMENT_FWD@" type="data" format="fastq,fastq.gz" multiple="@MULTIPLE@" label="Short read data"/> | |
98 </when> | |
99 </conditional> | |
100 </xml> | |
101 | |
102 <!-- for filterAndTrim --> | |
103 <xml name="trimmers"> | |
104 <section name="trim" title="Trimming parameters"> | |
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"/> | |
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."/> | |
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"/> | |
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)"/> | |
109 </section> | |
110 </xml> | |
111 <xml name="filters"> | |
112 <section name="filter" title="Filtering parameters"> | |
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"/> | |
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"/> | |
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"/> | |
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"/> | |
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"/> | |
118 </section> | |
119 </xml> | |
120 | |
121 <xml name="errorEstimationFunction"> | |
122 <param name="errfoo" argument="errorEstimationFunction" type="select" label="Error function"> | |
123 <option value="loessErrfun">loess: Use a loess fit to estimate error rates from transition counts</option> | |
124 <option value="noqualErrfun">noqual: Estimate error rates for each type of transition while ignoring quality scores.</option> | |
125 <option value="PacBioErrfun">PacBio: Estimate error rates from transition counts in PacBio CCS data.</option> | |
126 </param> | |
127 </xml> | |
128 <token name="@HELP_OVERVIEW@"><![CDATA[ | |
129 Overview | |
130 ........ | |
131 | |
132 The intended use of the dada2 tools for paired sequencing data is shown in the following image. | |
133 | |
134 .. image:: pairpipe.png | |
135 | |
136 Note: In particular for the analysis of paired collections the collections should be sorted lexicographical | |
137 before the analysis. | |
138 | |
139 For single end data you the steps "Unzip collection" and "mergePairs" are not necessary. | |
140 | |
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) | |
142 ]]></token> | |
143 </macros> |