Repository revision
9:947faa8b3205

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

Remove.lineage tool metadata
Miscellaneous
Picks by taxon
mothur_remove_lineage
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/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_remove_lineage/mothur_remove_lineage/1.39.5.0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/mothur_remove_lineage/mothur_remove_lineage/1.36.1.0
mothur_remove_lineage
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 '$file.taxonomy' file.taxonomy.dat &&
#if $file.filetype == "useconstaxonomy":
    ln -s '$file.shared' file.shared.dat &&
    ln -s '$file.list' file.list.dat &&
#end if
ln -s '$fasta_in' fasta_in.dat &&
ln -s '$group_in' group_in.dat &&
ln -s '$alignreport_in' alignreport_in.dat &&
ln -s '$list_in' list_in.dat &&
ln -s '$name_in' name_in.dat &&
ln -s '$count' count.dat &&

echo 'remove.lineage(
    #if $file.filetype == "usetaxonomy":
        taxonomy=file.taxonomy.dat
    #else
        constaxonomy=file.taxonomy.dat
        #if $file.shared:
            ,shared=file.shared.dat
        #end if
        #if $file.list:
            ,list=file.list.dat
        #end if
    #end if
    #if $file.taxons:
        #set taxonstring=str($file.taxons).replace(",","-")
        ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxonstring ))'"'
    #elif $taxon:
        ,taxon='"'$re.sub("(\s|,)+",",",$re.sub("\(\d+\)","", $taxon.value )).replace(",","-")'"'
    #end if
    #if $fasta_in:
        ,fasta=fasta_in.dat
    #end if
    #if $group_in:
        ,group=group_in.dat
    #end if
    #if $alignreport_in:
        ,alignreport=alignreport_in.dat
    #end if
    #if $list_in:
        ,list=list_in.dat
    #end if
    #if $name_in:
        ,name=name_in.dat
        ,dups=$dups
    #end if
    #if $count:
        ,count=count.dat
    #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 file|taxonomy: abrecovery.pds.wang.taxonomy
file|filetype: usetaxonomy
taxon: Bacteria;Firmicutes;
count: amazon.count_table
name: value
name: value
abrecovery.pds.wang.taxonomy
amazon.count_table
value
Test-2 file|taxonomy: abrecovery.pds.wang.taxonomy
file|filetype: usetaxonomy
taxon: Bacteria;Firmicutes;,Bacteria;Actinobacteria;
fasta_in: abrecovery.fasta
group_in: abrecovery.groups
alignreport_in: Mock_S280_L001_R1_001_small.contigs.report
list_in: amazon.an.list
name_in: abrecovery.names
name: value
name: value
name: value
name: value
name: value
abrecovery.pds.wang.taxonomy
abrecovery.fasta
abrecovery.groups
Mock_S280_L001_R1_001_small.contigs.report
amazon.an.list
abrecovery.names
value
Test-3 file|taxonomy: abrecovery.pds.wang.taxonomy
file|taxons: ['Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Dorea(99);', 'Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Roseburia(47);']
file|filetype: usetaxonomy
name: value
abrecovery.pds.wang.taxonomy
value
Test-4 file|taxonomy: example.constaxonomy
file|filetype: useconstaxonomy
taxon: Bacteria;Bacteroidetes;
name: value
example.constaxonomy
value
Test-5 file|taxonomy: example.constaxonomy
file|taxons: ['Bacteria(100);Firmicutes(100);Clostridia(70);Clostridiales(70);Lachnospiraceae(51);unclassified;', 'Bacteria(100);Proteobacteria(100);Gammaproteobacteria(100);unclassified;unclassified;unclassified;']
file|filetype: useconstaxonomy
name: value
example.constaxonomy
value