| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_fastq_info/mothur_fastq_info/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_fastq_info/mothur_fastq_info/1.36.1.0 |
| mothur_fastq_info |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| mothur | 1.39.5 | package |
| Additional information about this tool |
set -o pipefail; export TERM=vt100;
## create symlinks to input datasets
ln -s '$fastq' fastq.dat &&
#if $oligo.add == "yes":
ln -s '$oligo.oligos' oligo.oligos.dat &&
#end if
echo 'fastq.info(
fastq=fastq.dat,
pacbio=$pacbio,
format=$format
#if $oligo.add == "yes":
,oligos=oligo.oligos.dat
,bdiffs=$oligo.bdiffs
,pdiffs=$oligo.pdiffs
,tdiffs=$oligo.tdiffs
,ldiffs=$oligo.ldiffs
,sdiffs=$oligo.sdiffs
#end if
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
## rename some outputs
#if $oligo.add == "yes":
&& mv fastq.scrap.fasta scrap.fasta
&& mv fastq.scrap.qual scrap.qual
#end if
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
fastq: Mock_S280_L001_R1_001_small.fastq pacbio: False format: sanger oligo|add: no savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.fastq value |
| Test-2 |
fastq: Mock_S280_L001_R1_001_small.fastq pacbio: False format: sanger oligo|oligos: GQY1XT001.oligos oligo|bdiffs: 1 oligo|pdiffs: 3 oligo|tdiffs: 3 oligo|ldiffs: 3 oligo|sdiffs: 7 oligo|add: yes savelog: True |
name: value name: value name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.fastq GQY1XT001.oligos value |
| Test-3 |
fastq: Mock_S280_L001_R1_001_small.fastq pacbio: False format: sanger oligo|oligos: HMPv5-v3_1368-1369.oligos oligo|bdiffs: 1 oligo|pdiffs: 3 oligo|tdiffs: 3 oligo|ldiffs: 3 oligo|sdiffs: 7 oligo|add: yes savelog: True |
name: value name: value name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.fastq HMPv5-v3_1368-1369.oligos value |