Mercurial > repos > matthias > dada2_makesequencetable

comparison dada2_makeSequenceTable.xml @ 5:ec4a183cc713 draft

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
author matthias
date Sun, 05 May 2019 12:37:14 -0400
parents c3834c230b0a
children 31e8d1265580
comparison
equal deleted inserted replaced
4:383501d6aeb0 5:ec4a183cc713
9 Rscript '$dada2_script' 9 Rscript '$dada2_script'
10 ]]></command> 10 ]]></command>
11 <configfiles> 11 <configfiles>
12 <configfile name="dada2_script"><![CDATA[ 12 <configfile name="dada2_script"><![CDATA[
13 @READ_FOO@ 13 @READ_FOO@
14 @WRITE_FOO@
14 15
15 library(dada2, quietly=T) 16 library(dada2, quietly=T)
16 #if $plot == "yes" 17 #if $plot == "yes"
17 library(ggplot2, quietly=T) 18 library(ggplot2, quietly=T)
18 #end if 19 #end if
19 20
20 samples <- list() 21 samples <- list()
21 #for $s in $samples: 22 #for $s in $samples:
22 #if $len($samples) == 1
23 samples <- readRDS('$s')
24 #else
25 samples[["$s.element_identifier"]] <- readRDS('$s') 23 samples[["$s.element_identifier"]] <- readRDS('$s')
26 #end if
27 #end for 24 #end for
28 ## make sequence table 25
29 seqtab <- makeSequenceTable(samples, orderBy = "$orderBy") 26 seqtab <- makeSequenceTable(samples, orderBy = "$orderBy")
30
31 27
32 reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum) 28 reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
33 df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen) 29 df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen)
34 30
35 #if $plot == "yes" 31 #if $plot == "yes"
43 bequiet <- dev.off() 39 bequiet <- dev.off()
44 #end if 40 #end if
45 41
46 ## filter by seqlengths 42 ## filter by seqlengths
47 #if $filter_cond.filter_select != "no" 43 #if $filter_cond.filter_select != "no"
48 seqtab <- seqtab[, nchar(colnames(seqtab)) %in% seq($filter_cond.min, $filter_cond.max)] 44 seqtab <- seqtab[, nchar(colnames(seqtab)) %in% seq($filter_cond.min, $filter_cond.max), drop=F]
49 #end if 45 #end if
50 46 write.data( seqtab, '$stable', "dada2_sequencetable" )
51 write.table(seqtab, "$stable", quote=F, sep="\t", row.names = T, col.names = NA)
52 ]]></configfile> 47 ]]></configfile>
53 </configfiles> 48 </configfiles>
54 <inputs> 49 <inputs>
55 <param name="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" /> 50 <param argument="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" />
56 <param argument="orderBy" type="select" label="Column order"> 51 <param argument="orderBy" type="select" label="Column order">
57 <option value="abundance">abundance</option> 52 <option value="abundance">abundance</option>
58 <option value="nsamples">nsamples</option> 53 <option value="nsamples">nsamples</option>
59 </param> 54 </param>
60 <conditional name="filter_cond"> 55 <conditional name="filter_cond">
75 <data name="plot_output" format="pdf" label="${tool.name} on ${on_string}: sequence length distribution"> 70 <data name="plot_output" format="pdf" label="${tool.name} on ${on_string}: sequence length distribution">
76 <filter>plot</filter> 71 <filter>plot</filter>
77 </data> 72 </data>
78 </outputs> 73 </outputs>
79 <tests> 74 <tests>
80 <test> 75 <test expect_num_outputs="2">
81 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/> 76 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
77 <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" />
78 <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" />
79 </test>
80 <test expect_num_outputs="1">
81 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
82 <param name="filter_cond|filter_select" value="minmax"/>
83 <param name="filter_cond|min" value="200"/>
84 <param name="filter_cond|max" value="300"/>
85 <param name="plot" value="no" />
82 <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" /> 86 <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" />
83 </test> 87 </test>
84 </tests> 88 </tests>
85 <help><![CDATA[ 89 <help><![CDATA[
86 Description 90 Description