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 |