Repository revision
9:09e3b0966a11

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

Sffinfo tool metadata
Miscellaneous
Sffinfo
Summarize the quality of sequences
mothur_sffinfo
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sffinfo/mothur_sffinfo/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_sffinfo/mothur_sffinfo/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_sffinfo/mothur_sffinfo/1.36.1.0
mothur_sffinfo
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 '$sff' sff.dat &&
ln -s '$accnos' accnos.dat &&
#if $oligo.add == "yes":
    ln -s '$oligo.oligos' oligo.oligos.dat &&
#end if

echo 'sffinfo(
    sff=sff.dat,
    fasta=$fasta,
    qfile=$qfile,
    $sfftxt
    flow=$flow,
    trim=$trim
    #if $accnos:
        ,accnos=accnos.dat
    #end if
    #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
    
None
False
Functional tests
name inputs outputs required files
Test-1 sff: Fasting_Example1.sff
sfftxt: True
savelog: True
name: value
name: value
name: value
name: value
name: value
Fasting_Example1.sff
value
Test-2 sff: Fasting_Example1.sff
oligo|oligos: GQY1XT001.oligos
oligo|add: yes
savelog: True
name: value
name: value
name: value
name: value
name: value
Fasting_Example1.sff
GQY1XT001.oligos
value