Revision: 5:a9f4a217dcd6

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/1.20+galaxy0

Version: 1.20+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/1.20+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.20+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/dada2_filterandtrim/dada2_filterAndTrim/1.18+galaxy0

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

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	1.20	package

Functional tests

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