Mercurial > repos > iuc > dada2_plotcomplexity
diff dada2_plotComplexity.xml @ 11:224abe7c80ed draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 commit f65944aa0547c2fbe4b746cf443c85b2a76e9a48
| author | iuc |
|---|---|
| date | Sat, 20 Dec 2025 14:15:33 +0000 |
| parents | 6f06d501b7e6 |
| children |
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--- a/dada2_plotComplexity.xml Tue Feb 11 23:26:21 2025 +0000 +++ b/dada2_plotComplexity.xml Sat Dec 20 14:15:33 2025 +0000 @@ -23,9 +23,6 @@ ln -s '$batch_cond.paired_cond.reads.forward' forward/'$elid' && ln -s '$batch_cond.paired_cond.reads.reverse' reverse/'$elid' && #end if - #if $batch_cond.paired_cond.paired_select == "separate" - ln -s '$batch_cond.paired_cond.sdaer' reverse/'$elid' && - #end if #else #for $read in $batch_cond.paired_cond.reads: #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier)) @@ -36,12 +33,6 @@ ln -s '$read.reverse' reverse/'$elid' && #end if #end for - #if $batch_cond.paired_cond.paired_select == "separate" - #for $read in $batch_cond.paired_cond.sdaer: - #set elid = re.sub('[^\w\-\.]', '_', str($read.element_identifier)) - ln -s '$read' reverse/'$elid' && - #end for - #end if #end if Rscript --slave '$dada2_script' @@ -132,16 +123,6 @@ <output name="output_fwd" value="complexity_fwd.pdf" ftype="pdf" compare="sim_size" delta="200"/> <output name="output_rev" value="complexity_rev.pdf" ftype="pdf" compare="sim_size" delta="200"/> </test> - <!-- paired-separate joint, no-aggregate (sim_size because element ids differ) --> - <test expect_num_outputs="2"> - <param name="batch_cond|batch_select" value="joint"/> - <param name="batch_cond|paired_cond|paired_select" value="separate"/> - <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D141_S207_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> - <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz,F3D141_S207_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> - <param name="batch_cond|aggregate" value="FALSE"/> - <output name="output_fwd" value="complexity_fwd.pdf" ftype="pdf" compare="sim_size" delta="200"/> - <output name="output_rev" value="complexity_rev.pdf" ftype="pdf" compare="sim_size" delta="200"/> - </test> <!-- single, non-batch, aggregate, small sample --> <test expect_num_outputs="1"> <param name="batch_cond|batch_select" value="joint"/> @@ -165,15 +146,6 @@ <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/> <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/> </test> - <!-- paired-separate batch (sim_size because element ids differ)--> - <test expect_num_outputs="2"> - <param name="batch_cond|batch_select" value="batch"/> - <param name="batch_cond|paired_cond|paired_select" value="separate"/> - <param name="batch_cond|paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> - <param name="batch_cond|paired_cond|sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> - <output name="output_fwd" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/> - <output name="output_rev" value="complexity.pdf" ftype="pdf" compare="sim_size" delta="200"/> - </test> <!-- single, batch --> <test expect_num_outputs="1"> <param name="batch_cond|batch_select" value="batch"/>