| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_sra/mothur_make_sra/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_sra/mothur_make_sra/1.36.1.0 |
| mothur_make_sra |
| 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 '$project' project.dat &&
ln -s '$sff' sff.dat &&
ln -s '$oligos' oligos.dat &&
ln -s '$mimark' mimark.dat &&
ln -s '$fastq' fastq.dat &&
echo 'make.sra(
project=project.dat,
sff=sff.dat,
oligos=oligos.dat,
mimark=mimark.dat,
#if $fastq:
fastq=fastq.dat,
#end if
bdiffs=$bdiffs,
pdiffs=$pdiffs,
tdiffs=$tdiffs,
ldiffs=$ldiffs,
sdiffs=$sdiffs,
checkorient=$checkorient,
orientation=$orientation,
platform=$platform,
instrument=$instrument,
libstrategy=$libstrategy,
libselection=$libselection,
libsource=$libsource,
datatype=$datatype,
trim=$trim,
includescrap=$includescrap
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
project: makesra.project sff: Fasting_Example1.sff oligos: GQY1XT001.oligos mimark: biosample.tsv savelog: True |
name: value name: value name: value name: value name: value name: value |
makesra.project Fasting_Example1.sff GQY1XT001.oligos biosample.tsv value |