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comparison macros.xml @ 0:de5c51e1c190 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
author matthias
date Fri, 08 Mar 2019 06:35:24 -0500
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children 4095456821e2
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-1:000000000000 0:de5c51e1c190
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
10 <token name="@DADA2_VERSION@">1.10.0</token>
11 <token name="@WRAPPER_VERSION@">0</token>
12
13 <xml name="version_command">
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: ")
16 ]]></version_command>
17 </xml>
18
19 echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
20
21 <xml name="citations">
22 <citations>
23 <citation type="doi">10.1038/nmeth.3869</citation>
24 </citations>
25 </xml>
26
27 <token name="@DADA_UNIQUES@">dada2_derep,dada2_dada,dada2_mergepairs</token>
28
29 <token name="@READ_FOO@"><![CDATA[
30 #def read_data($dataset)
31 #if $dataset.is_of_type('dada2_derep')
32 readRDS(file.path('$dataset.extra_files_path', 'Rdata'))
33 #else if $dataset.is_of_type('dada2_dada')
34 readRDS('$dataset')
35 #else if $dataset.is_of_type('dada2_sequencetable')
36 as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) )
37 #else if $dataset.is_of_type('dada2_mergepairs')
38 read.table('$dataset', header=T, sep="\t" )
39 #else if $dataset.is_of_type('tabular')
40 read.table('$dataset', header=T, sep="\t", row.names=1 )
41 #else
42 #raise Exception("error: unknown input type")
43 #end if
44 #end def
45 ]]></token>
46 <!-- for filterAndTrim -->
47 <xml name="trimmers">
48 <section name="trim" title="trimming parameters">
49 <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"/>
50 <param name="truncLen" type="integer" value="0" min="0" label="Truncate read length" help=""/>
51 <param name="trimLeft" type="integer" value="0" min="0" label="Remove nucleotides from start" help=""/>
52 <param name="trimRight" type="integer" value="0" min="0" label="Remove nucleotides from end" help=""/>
53 </section>
54 </xml>
55 <xml name="filters">
56 <section name="filter" title="filtering parameters">
57 <param name="maxLen" type="integer" value="" optional="true" min="0" label="Remove reads longer than" help=""/>
58 <param name="minLen" type="integer" value="20" min="0" label="Remove reads shorter than" help=""/>
59 <param name="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help=""/>
60 <param name="minQ" type="integer" value="0" min="0" label="Remove reads containing quality" help=""/>
61 <param name="maxEE" type="integer" value="" optional="true" min="0" label="Remove reads by expected errors" help=""/>
62 </section>
63 </xml>
64
65
66 <xml name="errorEstimationFunction">
67 <param name="errfoo" type="select" label="Error function">
68 <option value="loessErrfun">loess</option>
69 <option value="noqualErrfun">noqual</option>
70 <option value="PacBioErrfun">PacBio</option>
71 </param>
72 </xml>
73
74
75 </macros>