Mercurial > repos > matthias > dada2_learnerrors

comparison macros.xml @ 3:10141f4eaae9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
author matthias
date Mon, 29 Apr 2019 08:56:03 -0400
parents 57eb7437f646
children 9aeea74a1fc9
comparison
equal deleted inserted replaced
2:57eb7437f646 3:10141f4eaae9
6 <yield/> 6 <yield/>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
9 9
10 <token name="@DADA2_VERSION@">1.10.0</token> 10 <token name="@DADA2_VERSION@">1.10.0</token>
11 <token name="@WRAPPER_VERSION@">0</token> 11 <token name="@WRAPPER_VERSION@">1</token>
12 12
13 <xml name="version_command"> 13 <xml name="version_command">
14 <version_command><![CDATA[ 14 <version_command><![CDATA[
15 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: ") 15 echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
16 ]]></version_command> 16 ]]></version_command>
17 </xml> 17 </xml>
18 18
19 <xml name="citations"> 19 <xml name="citations">
20 <citations> 20 <citations>
21 <citation type="doi">10.1038/nmeth.3869</citation> 21 <citation type="doi">10.1038/nmeth.3869</citation>
22 <yield/>
22 </citations> 23 </citations>
23 </xml> 24 </xml>
24 25
25 <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token> 26 <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>
26 27
27 <token name="@READ_FOO@"><![CDATA[ 28 <token name="@READ_FOO@"><![CDATA[
28 #def read_data($dataset) 29 #def read_data($dataset)
29 #if $dataset.is_of_type('dada2_derep') 30 #if $dataset.is_of_type('dada2_derep')
30 readRDS(file.path('$dataset.extra_files_path', 'Rdata')) 31 readRDS('$dataset)
31 #else if $dataset.is_of_type('dada2_dada') 32 #else if $dataset.is_of_type('dada2_dada')
32 readRDS('$dataset') 33 readRDS('$dataset')
33 #else if $dataset.is_of_type('dada2_sequencetable') 34 #else if $dataset.is_of_type('dada2_sequencetable')
34 as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) ) 35 as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) )
35 #else if $dataset.is_of_type('dada2_mergepairs') 36 #else if $dataset.is_of_type('dada2_mergepairs')
36 read.table('$dataset', header=T, sep="\t" ) 37 readRDS('$dataset')
37 #else if $dataset.is_of_type('tabular') 38 #else if $dataset.is_of_type('tabular')
38 read.table('$dataset', header=T, sep="\t", row.names=1 ) 39 read.table('$dataset', header=T, sep="\t", row.names=1 )
39 #else 40 #else
40 #raise Exception("error: unknown input type") 41 #raise Exception("error: unknown input type")
41 #end if 42 #end if
42 #end def 43 #end def
43 ]]></token> 44 ]]></token>
44 <!-- for filterAndTrim --> 45 <!-- for filterAndTrim -->
45 <xml name="trimmers"> 46 <xml name="trimmers">
46 <section name="trim" title="Trimming parameters"> 47 <section name="trim" title="Trimming parameters">
47 <param name="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"/> 48 <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"/>
48 <param name="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."/> 49 <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."/>
49 <param name="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"/> 50 <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"/>
50 <param name="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."/> 51 <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."/>
51 </section> 52 </section>
52 </xml> 53 </xml>
53 <xml name="filters"> 54 <xml name="filters">
54 <section name="filter" title="Filtering parameters"> 55 <section name="filter" title="Filtering parameters">
55 <param name="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"/> 56 <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"/>
56 <param name="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/> 57 <param argument="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/>
57 <param name="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"/> 58 <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"/>
58 <param name="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"/> 59 <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"/>
59 <param name="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"/> 60 <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"/>
60 </section> 61 </section>
61 </xml> 62 </xml>
62 63
63 <xml name="errorEstimationFunction"> 64 <xml name="errorEstimationFunction">
64 <param name="errfoo" type="select" label="Error function"> 65 <param name="errfoo" argument="errorEstimationFunction" type="select" label="Error function">
65 <option value="loessErrfun">loess</option> 66 <option value="loessErrfun">loess</option>
66 <option value="noqualErrfun">noqual</option> 67 <option value="noqualErrfun">noqual</option>
67 <option value="PacBioErrfun">PacBio</option> 68 <option value="PacBioErrfun">PacBio</option>
68 </param> 69 </param>
69 </xml> 70 </xml>
71 <token name="@HELP_OVERVIEW@"><![CDATA[
72 Overview
73 ........
70 74
75 The intended use of the dada2 tools for paired sequencing data is shown in the following image.
71 76
77 .. image:: pairpipe.png
78
79 For single end data you the steps "Unzip collection" and "mergePairs" are not necessary.
80
81 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)
82 ]]></token>
72 </macros> 83 </macros>