| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.28+galaxy0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.20+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.20+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.18+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.16+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.14+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.12+galaxy1 |
| toolshed.g2.bx.psu.edu/repos/iuc/dada2_plotqualityprofile/dada2_plotQualityProfile/1.12+galaxy0 |
| dada2_plotQualityProfile |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| bioconductor-dada2 | 1.28 | package |
| Additional information about this tool |
##name files by linking
#import re
mkdir forward &&
#if $batch_cond.paired_cond.paired_select != "single"
mkdir reverse &&
#end if
#if $batch_cond.batch_select == "batch":
#set elid = re.sub('[^\w\-\.]', '_', str($batch_cond.paired_cond.reads.element_identifier))
#if $batch_cond.paired_cond.paired_select != "paired"
ln -s '$batch_cond.paired_cond.reads' forward/'$elid' &&
#else
ln -s '$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))
#if $batch_cond.paired_cond.paired_select != "paired"
ln -s '$read' forward/'$elid' &&
#else
ln -s '$read.forward' forward/'$elid' &&
ln -s '$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'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
batch_cond|paired_cond|reads: list:paired collection batch_cond|paired_cond|paired_select: paired batch_cond|aggregate: False batch_cond|batch_select: joint |
name: value name: value |
F3D0_S188_L001_R1_001.fastq.gz F3D0_S188_L001_R2_001.fastq.gz F3D141_S207_L001_R1_001.fastq.gz F3D141_S207_L001_R2_001.fastq.gz value |
| Test-2 |
batch_cond|paired_cond|reads: ['F3D0_S188_L001_R1_001.fastq.gz', 'F3D141_S207_L001_R1_001.fastq.gz'] batch_cond|paired_cond|sdaer: ['F3D0_S188_L001_R2_001.fastq.gz', 'F3D141_S207_L001_R2_001.fastq.gz'] batch_cond|paired_cond|paired_select: separate batch_cond|aggregate: False batch_cond|batch_select: joint |
name: value name: value |
F3D0_S188_L001_R1_001.fastq.gz F3D141_S207_L001_R1_001.fastq.gz F3D0_S188_L001_R2_001.fastq.gz F3D141_S207_L001_R2_001.fastq.gz value |
| Test-3 |
batch_cond|paired_cond|reads: ['F3D0_S188_L001_R1_001.fastq.gz', 'F3D0_S188_L001_R2_001.fastq.gz'] batch_cond|paired_cond|paired_select: single batch_cond|aggregate: True batch_cond|batch_select: joint n: 10000 |
name: value |
F3D0_S188_L001_R1_001.fastq.gz F3D0_S188_L001_R2_001.fastq.gz value |
| Test-4 |
batch_cond|paired_cond|reads: paired collection batch_cond|paired_cond|paired_select: paired batch_cond|batch_select: batch |
name: value name: value |
F3D0_S188_L001_R1_001.fastq.gz F3D0_S188_L001_R2_001.fastq.gz value |
| Test-5 |
batch_cond|paired_cond|reads: F3D0_S188_L001_R1_001.fastq.gz batch_cond|paired_cond|sdaer: F3D0_S188_L001_R2_001.fastq.gz batch_cond|paired_cond|paired_select: separate batch_cond|batch_select: batch |
name: value name: value |
F3D0_S188_L001_R1_001.fastq.gz F3D0_S188_L001_R2_001.fastq.gz value |
| Test-6 |
batch_cond|paired_cond|reads: F3D0_S188_L001_R1_001.fastq.gz batch_cond|paired_cond|paired_select: single batch_cond|batch_select: batch n: 10000 |
name: value |
F3D0_S188_L001_R1_001.fastq.gz value |