Repository revision
9:305ce07a4b16

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

Get.oturep tool metadata
Miscellaneous
Get.oturep
Generate a fasta with a representative sequence for each OTU
mothur_get_oturep
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_oturep/mothur_get_oturep/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_get_oturep/mothur_get_oturep/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_get_oturep/mothur_get_oturep/1.36.1.0
mothur_get_oturep
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 '$otu' otu.dat &&
#if $method_condition.method_switch == "distance":
    ln -s '$method_condition.matrix_condition.dist' dist.dat &&
    ln -s '$method_condition.matrix_condition.nameOrCount' nameOrCount.dat &&
    ln -s '$method_condition.fasta' fasta.dat &&
    #if $method_condition.pick.type == "yes":
        ln -s '$method_condition.pick.group' group.dat &&
    #end if
#elif $method_condition.method_switch == "abundance":
    ln -s '$method_condition.nameOrCount' nameOrCount.dat &&
#end if

echo 'get.oturep(
    list=otu.dat,
    #if $sorted:
        sorted=$sorted,
    #end if
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $method_condition.method_switch == "distance":
        method=distance,
        #if $method_condition.matrix_condition.matrix_format == "column":
            column=dist.dat,
            #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"):
                name=nameOrCount.dat,
            #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"):
                count=nameOrCount.dat,
            #end if
        #elif $method_condition.matrix_condition.matrix_format == "phylip":
            phylip=dist.dat,
            #if $method_condition.matrix_condition.nameOrCount:
                #if $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.names"):
                    name=nameOrCount.dat,
                #elif $method_condition.matrix_condition.nameOrCount.is_of_type("mothur.count_table"):
                    count=nameOrCount.dat,
                #end if
            #end if
        #end if
        #if $method_condition.fasta:
            fasta=fasta.dat,
        #end if
        #if $method_condition.pick.type == "yes":
            #if $method_condition.pick.group:
                group=group.dat,
            #end if
            #if $method_condition.pick.groups:
                groups=${ str($method_condition.pick.groups).replace(",","-") },
            #end if
        #end if
        large=$method_condition.large
    #elif $method_condition.method_switch == "abundance":
        method=abundance,
        #if $method_condition.nameOrCount.is_of_type("mothur.names"):
            name=nameOrCount.dat
        #elif $method_condition.nameOrCount.is_of_type("mothur.count_table"):
            count=nameOrCount.dat
        #end if
    #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 otu: amazon.an.list
method_condition|matrix_condition|dist: 98_sq_phylip_amazon.dist
method_condition|matrix_condition|nameOrCount: amazon1.names
method_condition|matrix_condition|matrix_format: phylip
method_condition|method_switch: distance
savelog: True
name: value
amazon.an.list
98_sq_phylip_amazon.dist
amazon1.names
value
Test-2 otu: amazon.an.list
method_condition|matrix_condition|dist: amazon.pair.dist
method_condition|matrix_condition|nameOrCount: amazon1.names
method_condition|matrix_condition|matrix_format: column
method_condition|method_switch: distance
label: ['unique', '0.05', '0.27', '0.45']
savelog: True
name: value
amazon.an.list
amazon.pair.dist
amazon1.names
value
Test-3 otu: amazon.an.list
method_condition|matrix_condition|dist: 98_sq_phylip_amazon.dist
method_condition|matrix_condition|matrix_format: phylip
method_condition|fasta: amazon.fasta
method_condition|method_switch: distance
label: ['0.05', '0.27']
sorted: name
savelog: True
name: value
amazon.an.list
98_sq_phylip_amazon.dist
amazon.fasta
value
Test-4 otu: amazon.an.list
method_condition|matrix_condition|dist: amazon.pair.dist
method_condition|matrix_condition|nameOrCount: amazon1.names
method_condition|matrix_condition|matrix_format: column
method_condition|pick|group: amazon.groups
method_condition|pick|groups: ['forest', 'pasture']
method_condition|pick|type: yes
method_condition|method_switch: distance
label: ['unique', '0.05', '0.27', '0.45']
savelog: True
name: value
amazon.an.list
amazon.pair.dist
amazon1.names
amazon.groups
value
Test-5 otu: amazon.an.list
method_condition|matrix_condition|dist: 98_sq_phylip_amazon.dist
method_condition|matrix_condition|nameOrCount: amazon1.count_table
method_condition|matrix_condition|matrix_format: phylip
method_condition|method_switch: distance
label: ['unique', '0.05', '0.27']
savelog: True
name: value
amazon.an.list
98_sq_phylip_amazon.dist
amazon1.count_table
value
Test-6 otu: amazon.an.list
method_condition|nameOrCount: amazon1.count_table
method_condition|method_switch: abundance
label: ['0.27', 'unique']
sorted: name
savelog: True
name: value
amazon.an.list
amazon1.count_table
value