Mercurial > repos > iuc > dada2_dada
changeset 1:6b4ddc3b64bd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"
| author | iuc |
|---|---|
| date | Thu, 05 Dec 2019 17:59:37 -0500 |
| parents | ce4aec98949d |
| children | 2222f08c8316 |
| files | README.md dada2_dada.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, 10 insertions(+), 4 deletions(-) [+] |
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--- a/README.md Fri Nov 08 18:48:34 2019 -0500 +++ b/README.md Thu Dec 05 17:59:37 2019 -0500 @@ -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_dada.xml Fri Nov 08 18:48:34 2019 -0500 +++ b/dada2_dada.xml Thu Dec 05 17:59:37 2019 -0500 @@ -104,7 +104,7 @@ <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" /> <param name="err" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" /> <output_collection name="data_collection" type="list"> - <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_R1.Rdata" ftype="dada2_dada"/> + <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> </output_collection> </test> <!-- default, batch --> @@ -112,7 +112,7 @@ <param name="batch_cond|batch_select" value="yes"/> <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" /> <param name="err" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" /> - <output name="dada" value="dada_F3D0_R1.Rdata" ftype="dada2_dada" /> + <output name="dada" value="dada_F3D0_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> </test> <!-- test non-default options --> <test> @@ -121,7 +121,7 @@ <param name="batch_cond|pool" value="pseudo"/> <param name="err" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" /> <output_collection name="data_collection" type="list"> - <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_R1.Rdata" ftype="dada2_dada"/> + <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> </output_collection> </test> </tests>
--- a/macros.xml Fri Nov 08 18:48:34 2019 -0500 +++ b/macros.xml Thu Dec 05 17:59:37 2019 -0500 @@ -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[