| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.1.b |
| toolshed.g2.bx.psu.edu/repos/iuc/gecko/gecko/1.1 |
| gecko |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| gecko | 1.2 | package |
| Additional information about this tool |
#import re
#set $queryName=re.sub('/', '\\/', str($query.element_identifier))
#set $dbName=re.sub('/', '\\/', str($db.element_identifier))
cp $query query.fasta &&
cp $db db.fasta &&
workflow.sh query.fasta db.fasta $minlen $similarity $kmer 1 &&
rm -rf intermediateFiles &&
#if str($options['selection_mode']) == "alignments":
frags2align.sh results/query-db.frags query.fasta db.fasta results/query-db.txt &&
mv results/query-db.txt $alignments2 &&
#end if
sed -i 's/query.fasta/$queryName/g' results/query-db.csv &&
sed -i 's/db.fasta/$dbName/g' results/query-db.csv &&
mv results/query-db.csv $csv_output1 &&
rm -rf results
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
query: hyopneumoniae_16S.fasta db: flocculare_16S.fasta kmer: 8 minlen: 20 similarity: 50 options|selection_mode: noalignments |
name: value |
hyopneumoniae_16S.fasta flocculare_16S.fasta value |
| Test-2 |
query: hyopneumoniae_16S.fasta db: flocculare_16S.fasta kmer: 8 minlen: 20 similarity: 50 options|selection_mode: alignments |
name: value name: value |
hyopneumoniae_16S.fasta flocculare_16S.fasta value |
| Test-3 |
query: mycoplasma-232.fasta db: mycoplasma-7422.fasta kmer: 16 minlen: 50 similarity: 60 options|selection_mode: alignments |
name: value name: value |
mycoplasma-232.fasta mycoplasma-7422.fasta value |