Galaxy |

Count.seqs tool metadata

Miscellaneous

Name: Count.seqs

Description: (aka make.table) counts the number of sequences represented by the representative

Id: mothur_count_seqs

Guid: toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0

Version: 1.39.5.0

Version command string: mothur "#help()" | sed '7q;d' | cut -d" " -f2

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.39.5.0 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/mothur_count_seqs/mothur_count_seqs/1.36.1.0

mothur_count_seqs

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

mothur

1.39.5

package

Additional information about this tool

Command:

set -o pipefail; export TERM=vt100; 

## create symlinks to input datasets
ln -s '$name' name.dat &&
#if $grouping.use == "yes":
    ln -s '$grouping.group' grouping.group.dat &&
#end if

echo 'count.seqs(
    #if $grouping.use == "yes":
        group=grouping.group.dat,
        #if $grouping.groups:
            groups=${ str($grouping.groups).replace(",","-") },
        #end if
    #end if
    name=name.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

name: amazon.names
savelog: True

name: value
name: value

amazon.names
value

Test-2

name: amazon.names
grouping|group: amazon.groups
grouping|use: yes
savelog: True

name: value
name: value

amazon.names
amazon.groups
value

Test-3

name: amazon.names
grouping|group: amazon.groups
grouping|groups: pasture
grouping|use: yes
savelog: True

name: value
name: value

amazon.names
amazon.groups
value

Test-4

name: amazon.names
grouping|group: amazon.groups
grouping|groups: ['pasture', 'forest']
grouping|use: yes
savelog: True

name: value
name: value

amazon.names
amazon.groups
value