Miscellaneous |
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
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 |