Repository revision
9:5f66e6f7f6c0

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

Chimera.pintail tool metadata
Miscellaneous
Find putative chimeras using pintail
mothur_chimera_pintail
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_pintail/mothur_chimera_pintail/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_chimera_pintail/mothur_chimera_pintail/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_pintail/mothur_chimera_pintail/1.36.1.0
mothur_chimera_pintail
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 '$fasta' fasta.dat &&
ln -s '$alignment.reference' alignment.reference.dat &&
ln -s '$conservation' conservation.dat &&
ln -s '$quantile' quantile.dat &&
#if $mask_cond.source2 == "history":
    ln -s '$mask_cond.mask' mask.dat &&
#end if

echo 'chimera.pintail(
    fasta=fasta.dat,
    reference=alignment.reference.dat,
    filter=$filter,
    #if $mask_cond.source2 == "default":
        mask=default,
    #elif $mask_cond.source2 == "history":
        mask=mask.dat,
    #end if
    #if $conservation:
        conservation=conservation.dat,
    #end if
    #if $quantile:
        quantile=quantile.dat,
    #end if
    #if int($window) > 0:
        window=$window,
    #end if
    #if int($increment) > 0:
        increment=$increment,
    #end if
    processors='\${GALAXY_SLOTS:-8}'
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    
None
False
Functional tests
name inputs outputs required files
Test-1 fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.align_head
alignment|reference: HMP_MOCK.v35.align
alignment|source: hist
quantile: HMP_MOCK.v35.pintail.quan
window: 200
savelog: True
name: value
name: value
name: value
Mock_S280_L001_R1_001_small.trim.contigs.good.align_head
HMP_MOCK.v35.align
HMP_MOCK.v35.pintail.quan
value
Test-2 fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.align_head
alignment|reference: HMP_MOCK.v35.align
alignment|source: hist
mask_cond|source2: default
window: 200
savelog: True
name: value
name: value
name: value
name: value
Mock_S280_L001_R1_001_small.trim.contigs.good.align_head
HMP_MOCK.v35.align
value