| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_trim_flows/mothur_trim_flows/1.39.5.0 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_trim_flows/mothur_trim_flows/1.36.1.0 |
| mothur_trim_flows |
| 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 '$flow' flow.dat &&
#if $oligo.add == "yes":
ln -s '$oligo.oligos' oligo.oligos.dat &&
#end if
echo 'trim.flows(
flow=flow.dat,
minflows=$minflows,
maxflows=$maxflows,
#if $maxhomop:
maxhomop=$maxhomop,
#end if
order=$order,
signal=$signal,
noise=$noise,
#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
fasta=$fasta,
processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g' ## mothur trips over whitespace
| mothur
| tee mothur.out.log
## prevent these two files from being gathered into collection
&& mv flow.trim.flow flow.trim
&& mv flow.scrap.flow flow.scrap
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
flow: mock.flow savelog: True |
name: value name: value name: value name: value |
mock.flow value |
| Test-2 |
flow: testflow.flow oligo|oligos: GQY1XT001.oligos oligo|bdiffs: 10 oligo|pdiffs: 10 oligo|add: yes order: I fasta: True savelog: True |
name: value name: value name: value name: value name: value |
testflow.flow GQY1XT001.oligos value |