Revision: 2:23fc35093b11

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim

Miscellaneous

Name: dada2: filterAndTrim

Description: Filter and trim short read data

Id: dada2_filterAndTrim

Guid: toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.14+galaxy0

Version: 1.14+galaxy0

Version command string: echo $(R --version | grep version | grep -v GNU)", dada2 version" $(R --vanilla --slave -e "library(dada2); cat(sessionInfo()\$otherPkgs\$dada2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.16+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.14+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.12+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.12+galaxy0

dada2_filterAndTrim

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name	version	type
bioconductor-dada2	1.14	package

Functional tests

name	inputs	outputs	required files
Test-1	paired_cond|reads: paired collection paired_cond|paired_select: paired	attributes: name	F3D0_S188_L001_R1_001.fastq.gz F3D0_S188_L001_R2_001.fastq.gz name
Test-2	paired_cond|reads: F3D0_S188_L001_R1_001.fastq.gz paired_cond|sdaer: F3D0_S188_L001_R2_001.fastq.gz paired_cond|paired_select: separate	attributes: name attributes: name attributes: name	F3D0_S188_L001_R1_001.fastq.gz F3D0_S188_L001_R2_001.fastq.gz name
Test-3	paired_cond|reads: F3D0_S188_L001_R1_001.fastq.gz rmPhiX: True rmlowcomplex: 2 paired_cond|paired_select: single output_statistics: False orientFwd: TACGG	attributes: name	F3D0_S188_L001_R1_001.fastq.gz name
Test-4	paired_cond|reads: F3D0_S188_L001_R1_001.fastq.gz trim|truncQ: 30 trim|trimLeft: 150 paired_cond|paired_select: single trim|truncLen: 2 trim|trimRight: 2 output_statistics: False	attributes: name	F3D0_S188_L001_R1_001.fastq.gz name
Test-5	paired_cond|reads: F3D0_S188_L001_R1_001.fastq.gz filter|maxEE: 1 filter|minQ: 13 paired_cond|paired_select: single filter|maxN: 100 filter|minLen: 60 filter|maxLen: 255 output_statistics: False	attributes: name	F3D0_S188_L001_R1_001.fastq.gz name
Test-6	paired_cond|reads: paired collection seprev_cond|filter|maxEE: 1 seprev_cond|filter|maxLen: 255 seprev_cond|filter|maxN: 100 seprev_cond|filter|minLen: 60 seprev_cond|trim|truncLen: 2 seprev_cond|trim|truncQ: 30 paired_cond|paired_select: paired seprev_cond|filter|minQ: 13 seprev_cond|trim|trimLeft: 150 output_statistics: False seprev_cond|trim|trimRight: 2 seprev_cond|seprev_select: yes		F3D0_S188_L001_R1_001.fastq.gz F3D0_S188_L001_R2_001.fastq.gz
Test-7	paired_cond|reads: paired collection filter|minLen: 1000 output_statistics: False paired_cond|paired_select: paired		F3D0_S188_L001_R1_001.fastq.gz F3D0_S188_L001_R2_001.fastq.gz