Repository revision
10:23c1af22331b

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

Make.lookup tool metadata
Miscellaneous
Make.lookup
allows you to create custom lookup files for use with shhh.flows
mothur_make_lookup
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_lookup/mothur_make_lookup/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_lookup/mothur_make_lookup/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_lookup/mothur_make_lookup/1.36.1.0
mothur_make_lookup
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; 

#import re
## create symlinks to input datasets
ln -s '$reference.template' reference.template.dat &&
ln -s '$flow' flow.dat &&
ln -s '$error' error.dat &&

echo 'make.lookup(
    reference=reference.template.dat,
    flow=flow.dat,
    error=error.dat,
    order=$order,
    barcode=$re.sub("[^ACTG]","",str($barcode)),
    key=$re.sub("[^ACTG]","",str($key)),
    threshold=$threshold
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
None
False
Functional tests
name inputs outputs required files
Test-1 reference|template: HMP_MOCK.v35.align
reference|source: hist
flow: testflow.flow
error: Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary
savelog: True
 name: value
name: value
 HMP_MOCK.v35.align
testflow.flow
Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary
value
Test-2 reference|template: HMP_MOCK.v35.align
reference|source: hist
flow: testflow.flow
error: Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary
barcode: XAXAXCXCXGXTXGXTXC
key: XTXCXAXGX
savelog: True
 name: value
name: value
 HMP_MOCK.v35.align
testflow.flow
Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary
value