Mercurial > repos > iuc > dada2_makesequencetable

comparison dada2_makeSequenceTable.xml @ 1:9ccec6ed8e82 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
author iuc
date Thu, 05 Dec 2019 18:00:38 -0500
parents 6e0946238688
children 99c6929236fa
comparison
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0:6e0946238688 1:9ccec6ed8e82
13 <configfile name="dada2_script"><![CDATA[ 13 <configfile name="dada2_script"><![CDATA[
14 @READ_FOO@ 14 @READ_FOO@
15 @WRITE_FOO@ 15 @WRITE_FOO@
16 16
17 library(dada2, quietly=T) 17 library(dada2, quietly=T)
18 #if $plot == "yes" 18 #if $plot
19 library(ggplot2, quietly=T) 19 library(ggplot2, quietly=T)
20 #end if 20 #end if
21 21
22 samples <- list() 22 samples <- list()
23 #for $s in $samples: 23 #for $s in $samples:
27 seqtab <- makeSequenceTable(samples, orderBy = "$orderBy") 27 seqtab <- makeSequenceTable(samples, orderBy = "$orderBy")
28 28
29 reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum) 29 reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
30 df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen) 30 df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen)
31 31
32 #if $plot == "yes" 32 #if $plot
33 pdf( '$plot_output' ) 33 pdf( '$plot_output' )
34 ggplot(data=df, aes(x=length, y=count)) + 34 ggplot(data=df, aes(x=length, y=count)) +
35 geom_col() + 35 geom_col() +
36 #if $filter_cond.filter_select != "no" 36 #if $filter_cond.filter_select != "no"
37 geom_vline( xintercept=c($filter_cond.min-0.5, $filter_cond.max+0.5) ) + 37 geom_vline( xintercept=c($filter_cond.min-0.5, $filter_cond.max+0.5) ) +
73 </data> 73 </data>
74 </outputs> 74 </outputs>
75 <tests> 75 <tests>
76 <test expect_num_outputs="2"> 76 <test expect_num_outputs="2">
77 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/> 77 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
78 <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" lines_diff="2"/> 78 <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" lines_diff="2"/>
79 <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" /> 79 <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" compare="sim_size" delta="3000" />
80 </test> 80 </test>
81 <test expect_num_outputs="1"> 81 <test expect_num_outputs="1">
82 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/> 82 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
83 <param name="filter_cond|filter_select" value="minmax"/> 83 <param name="filter_cond|filter_select" value="minmax"/>
84 <param name="filter_cond|min" value="200"/> 84 <param name="filter_cond|min" value="200"/>