| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.39.5.0 |
| toolshed.g2.bx.psu.edu/repos/iuc/mothur_screen_seqs/mothur_screen_seqs/1.36.1.0 |
| mothur_screen_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 '$fasta' fasta.dat &&
ln -s '$names' names.dat &&
ln -s '$groups' groups.dat &&
ln -s '$qfile' qfile.dat &&
ln -s '$count' count.dat &&
ln -s '$taxonomy' taxonomy.dat &&
ln -s '$summary' summary.dat &&
#if $contigsrep.usecontigs == "yes":
ln -s '$contigsrep.contigsreport' contigsreport.dat &&
#end if
#if $alignrep.usealign == "yes":
ln -s '$alignrep.alignreport' alignreport.dat &&
#end if
echo 'screen.seqs(
fasta=fasta.dat
#if int($start) > -1:
,start=$start
#end if
#if int($end) > -1:
,end=$end
#end if
#if int($minlength) > -1:
,minlength=$minlength
#end if
#if int($maxlength) > -1:
,maxlength=$maxlength
#end if
#if int($maxambig) > -1:
,maxambig=$maxambig
#end if
#if int($maxhomop) > -1:
,maxhomop=$maxhomop
#end if
#if int($criteria) > -1:
,criteria=$criteria
#end if
#if $optimize:
,optimize=#echo str($optimize).replace(',','-') #
#end if
#if $qfile:
,qfile=qfile.dat
#end if
#if $names:
,name=names.dat
#end if
#if $groups:
,group=groups.dat
#end if
#if $taxonomy:
,taxonomy=taxonomy.dat
#end if
#if $count:
,count=count.dat
#end if
#if $summary:
,summary=summary.dat
#end if
#if $contigsrep.usecontigs == "yes":
,contigsreport=contigsreport.dat
,minoverlap=$contigsrep.minoverlap
,ostart=$contigsrep.ostart
,oend=$contigsrep.oend
,mismatches=$contigsrep.mismatches
#end if
#if $alignrep.usealign == "yes":
,alignreport=alignreport.dat
,minsim=$alignrep.minsim
,minscore=$alignrep.minscore
,maxinsert=$alignrep.maxinsert
#end if
,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: Mock_S280_L001_R1_001_small.trim.contigs.fasta maxlength: 275 maxambig: 0 savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.fasta value |
| Test-2 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.fasta criteria: 50 optimize: ['minlength', 'maxlength', 'maxhomop'] savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.fasta value |
| Test-3 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.fasta criteria: 50 optimize: ['end', 'maxambig'] savelog: True |
name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.fasta value |
| Test-4 |
fasta: amazon.fasta maxlength: 500 maxambig: 0 count: amazon1.count_table savelog: True |
name: value name: value name: value name: value |
amazon.fasta amazon1.count_table value |
| Test-5 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.fasta maxlength: 275 maxambig: 0 contigsrep|contigsreport: Mock_S280_L001_R1_001_small.contigs.report contigsrep|mismatches: 18 contigsrep|usecontigs: yes savelog: True |
name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.fasta Mock_S280_L001_R1_001_small.contigs.report value |
| Test-6 |
fasta: Mock_S280_L001_R1_001_small.trim.contigs.good.fasta maxlength: 275 maxambig: 0 alignrep|alignreport: Mock_S280_L001_R1_001_small.trim.contigs.good.align.report alignrep|minscore: 100 alignrep|usealign: yes savelog: True |
name: value name: value name: value name: value |
Mock_S280_L001_R1_001_small.trim.contigs.good.fasta Mock_S280_L001_R1_001_small.trim.contigs.good.align.report value |