Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_uchime/mothur_chimera_uchime/1.39.5.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/mothur_chimera_uchime/mothur_chimera_uchime/1.36.1.0 |
mothur_chimera_uchime |
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 && #if $template.source == "self": ln -s '$template.count' template.count.dat && ln -s '$template.group' template.group.dat && #elif $template.source == "names": ln -s '$template.name' template.name.dat && #else: ln -s '$template.reference' template.reference.dat && #end if echo 'chimera.uchime( fasta=fasta.dat, #if $template.source == "self": reference=self, #if float($template.abskew) > 0: abskew=$template.abskew, #end if #if $template.group: group=template.group.dat, #end if #if $template.count: count=template.count.dat, #end if #elif $template.source == "names": name=template.name.dat, #else: reference=template.reference.dat, #end if minh=$minh, mindiv=$mindiv, xn=$xn, dn=$dn, xa=$xa, chunks=$chunks, minchunk=$minchunk, #if $idsmoothwindow: idsmoothwindow=$idsmoothwindow, #end if maxp=$maxp, minlen=$minlen, maxlen=$maxlen, skipgaps=$skipgaps, skipgaps2=$skipgaps2, #if $alignment.ucl == "local": ucl=true, #if $alignment.queryfract: queryfract=$alignment.queryfract, #end if #end if dereplicate=$dereplicate, chimealns=$chimealns, processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log 2>&1 ## uchime component writes output to stderr
Functional tests |
name | inputs | outputs | required files |
Test-1 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera template|reference: HMP_MOCK.v35.align template|source: hist savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera HMP_MOCK.v35.align value |
Test-2 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.align_head template|source: self savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.align_head value |
Test-3 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera template|reference: HMP_MOCK.v35.align template|source: hist chimealns: True savelog: True |
name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.align_head_withchimera HMP_MOCK.v35.align value |