Mercurial > repos > iuc > dada2_makesequencetable
changeset 1:12ca33471ce7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
| author | iuc |
|---|---|
| date | Thu, 05 Dec 2019 22:55:59 +0000 |
| parents | a877c9342d80 |
| children | f5318fa1d80d |
| files | README.md dada2_makeSequenceTable.xml macros.xml test-data/complexity.pdf test-data/derepFastq_F3D0_R1.Rdata test-data/derepFastq_F3D0_R2.Rdata test-data/learnErrors_F3D0_R1.pdf test-data/learnErrors_F3D0_R2.pdf test-data/makeSequenceTable_F3D0.pdf test-data/qualityProfile.pdf |
| diffstat | 10 files changed, 11 insertions(+), 5 deletions(-) [+] |
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--- a/README.md Fri Nov 08 18:43:58 2019 -0500 +++ b/README.md Thu Dec 05 22:55:59 2019 +0000 @@ -1,15 +1,21 @@ Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html. +- assignTaxonomyAddspecies - filterAndTrim - learnErrors - dada - mergePairs - makeSequenceTable +- plotComplexity +- plotQualityProfile - removeBimeraDenovo +- seqCounts Installation ============ +A conda release >=4.6 is needed so that the bioconductor-dada2 conda environment can be installed correctly. + The dada2 wrappers can be installed via the toolshed. Since they use datatypes that have been introduced with Galaxy release 19.09 they won't work out of the box for older Galaxy releases. In order to run the tools you may either upgrade Galaxy or execute the following two steps:
--- a/dada2_makeSequenceTable.xml Fri Nov 08 18:43:58 2019 -0500 +++ b/dada2_makeSequenceTable.xml Thu Dec 05 22:55:59 2019 +0000 @@ -15,7 +15,7 @@ @WRITE_FOO@ library(dada2, quietly=T) -#if $plot == "yes" +#if $plot library(ggplot2, quietly=T) #end if @@ -29,7 +29,7 @@ reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum) df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen) -#if $plot == "yes" +#if $plot pdf( '$plot_output' ) ggplot(data=df, aes(x=length, y=count)) + geom_col() + @@ -75,8 +75,8 @@ <tests> <test expect_num_outputs="2"> <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/> - <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" lines_diff="2"/> - <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" /> + <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" lines_diff="2"/> + <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" compare="sim_size" delta="3000" /> </test> <test expect_num_outputs="1"> <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
--- a/macros.xml Fri Nov 08 18:43:58 2019 -0500 +++ b/macros.xml Thu Dec 05 22:55:59 2019 +0000 @@ -8,7 +8,7 @@ </xml> <token name="@DADA2_VERSION@">1.12</token> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@WRAPPER_VERSION@">1</token> <xml name="version_command"> <version_command><![CDATA[