Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pcr_seqs/mothur_pcr_seqs/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_pcr_seqs/mothur_pcr_seqs/1.36.1.0 |
mothur_pcr_seqs |
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 '$fasta' fasta.dat && ln -s '$name_in' name_in.dat && ln -s '$group_in' group_in.dat && ln -s '$taxonomy_in' taxonomy_in.dat && #if $trim.method == "oligos": ln -s '$trim.oligos' trim.oligos.dat && #elif $trim.method == "reference": ln -s '$trim.ecoli' trim.ecoli.dat && #end if echo 'pcr.seqs( fasta=fasta.dat, #if $name_in name=name_in.dat, #end if #if $group_in: group=group_in.dat, #end if #if $taxonomy_in: taxonomy=taxonomy_in.dat, #end if #if $trim.method == "oligos": oligos=trim.oligos.dat, nomatch=$trim.nomatch, $trim.keepprimer #elif $trim.method == "reference": ecoli=trim.ecoli.dat, #elif $trim.method == "position": start=$trim.start, #if $trim.end and int($trim.end) > 0: end=$trim.end, #end if #end if pdiffs=$pdiffs, rdiffs=$rdiffs, $keepdots processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log
Functional tests |
name | inputs | outputs | required files |
Test-1 |
fasta: amazon.align_head trim|start: 0 trim|end: 0 trim|method: position keepdots: True pdiffs: 0 savelog: True |
name: value name: value name: value |
amazon.align_head value |
Test-2 |
fasta: amazon.align_head trim|ecoli: amazon.align_head trim|method: reference keepdots: False name_in: amazon.align_head.names pdiffs: 2 savelog: True |
name: value name: value name: value name: value |
amazon.align_head amazon.align_head.names value |
Test-3 |
fasta: amazon.align_head trim|oligos: GQY1XT001.oligos trim|method: oligos taxonomy_in: amazon.wang.wang.taxonomy name_in: amazon.names group_in: amazon.groups savelog: True |
name: value name: value name: value name: value name: value name: value name: value |
amazon.align_head GQY1XT001.oligos amazon.wang.wang.taxonomy amazon.names amazon.groups value |