Mercurial > repos > iuc > dada2_makesequencetable
comparison dada2_makeSequenceTable.xml @ 1:9ccec6ed8e82 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
author | iuc |
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date | Thu, 05 Dec 2019 18:00:38 -0500 |
parents | 6e0946238688 |
children | 99c6929236fa |
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0:6e0946238688 | 1:9ccec6ed8e82 |
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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"/> |