Repository revision
9:f09c0a3bf8b9

Repository 'mothur_make_fastq'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_fastq

Make.fastq tool metadata
Miscellaneous
Make.fastq
Convert fasta and quality to fastq
mothur_make_fastq
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_fastq/mothur_make_fastq/1.39.5.0
1.39.5.0
mothur "#help()" | sed '7q;d' | cut -d" " -f2
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_fastq/mothur_make_fastq/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_fastq/mothur_make_fastq/1.36.1.0
mothur_make_fastq
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 '$fasta' fasta.dat &&
ln -s '$qfile' qfile.dat &&

echo 'make.fastq(
    fasta=fasta.dat,
    qfile=qfile.dat
    #if $chooseformat.use == "yes":
        ,format=${chooseformat.format}
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
Functional tests
name inputs outputs required files
Test-1 fasta: Mock_S280_L001_R1_001_small.trim.contigs.fasta
qfile: Mock_S280_L001_R1_001_small.trim.contigs.qual
savelog: True
name: value
name: value
Mock_S280_L001_R1_001_small.trim.contigs.fasta
Mock_S280_L001_R1_001_small.trim.contigs.qual
value
Test-2 fasta: Mock_S280_L001_R1_001_small.trim.contigs.fasta
qfile: Mock_S280_L001_R1_001_small.trim.contigs.qual
chooseformat|format: illumina
chooseformat|use: yes
savelog: True
name: value
name: value
Mock_S280_L001_R1_001_small.trim.contigs.fasta
Mock_S280_L001_R1_001_small.trim.contigs.qual
value