Mercurial > repos > iuc > dada2_dada
diff dada2_dada.xml @ 2:2222f08c8316 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
| author | iuc |
|---|---|
| date | Mon, 16 Mar 2020 07:34:56 -0400 |
| parents | 6b4ddc3b64bd |
| children | 84fd33a60b35 |
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--- a/dada2_dada.xml Thu Dec 05 17:59:37 2019 -0500 +++ b/dada2_dada.xml Mon Mar 16 07:34:56 2020 -0400 @@ -22,9 +22,12 @@ derep <- c() #if $batch_cond.batch_select == "no" +ids<-c() #for $d in $batch_cond.derep: derep <- c(derep, '$d') +ids <- c(ids, '$d.element_identifier') #end for +names(derep) <- ids #else derep <- c(derep, '$batch_cond.derep') #end if @@ -50,6 +53,11 @@ dada_result <- dada(derep, err, pool = pool, multithread = nthreads) +## in non batch mode the results of the samples are stored in a list +## (of dada class objects) these are stored in separate files (which +## then go into a collection). +## special case: for 1 sample the dada_result is not a list of dada +## objects but it is a dada object #if $batch_cond.batch_select == "no": #if len($batch_cond.derep) > 1: for( id in names(dada_result) ){ @@ -99,29 +107,30 @@ </outputs> <tests> <!-- default, non batch --> - <test> + <test expect_num_outputs="1"> <param name="batch_cond|batch_select" value="no"/> - <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" /> + <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz,filterAndTrim_F3D141_R1.fq.gz" ftype="fastq.gz" /> + <param name="err" value="learnErrors_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" compare="sim_size" delta="10000"/> + <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> + <element name="filterAndTrim_F3D141_R1.fq.gz" file="dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> </output_collection> </test> <!-- default, batch --> - <test> + <test expect_num_outputs="1"> <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" compare="sim_size" delta="10000"/> + <param name="err" value="learnErrors_R1.Rdata" ftype="dada2_errorrates" /> + <output name="dada" value="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> </test> <!-- test non-default options --> - <test> + <test expect_num_outputs="1"> <param name="batch_cond|batch_select" value="no"/> <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" /> <param name="batch_cond|pool" value="pseudo"/> - <param name="err" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" /> + <param name="err" value="learnErrors_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" compare="sim_size" delta="10000"/> + <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_S188_L001_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/> </output_collection> </test> </tests>