| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/get_species_taxids/2.14.1+galaxy2 (this tool) |
| toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/get_species_taxids/2.10.1+galaxy1 |
| get_species_taxids |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| blast | 2.14.1 | package |
| Additional information about this tool |
#if $type_cond.type_sel == 'names'
#for name in $type_cond.names.split(',')
taxid=\$(get_species_taxids.sh -n '$name' | grep Taxid | sed 's/Taxid\s*:\s*//') &&
if [ -z "\$taxid" ]; then
>&2 echo "could not find taxid for $name" && exit 1;
else
echo " $name -> \$taxid";
fi &&
get_species_taxids.sh -t "\$taxid" >> species_ids.txt &&
#end for
#else
#for taxid in $type_cond.ids.split(',')
get_species_taxids.sh -t "$taxid" >> species_ids.txt &&
#end for
#end if
sort -n -u species_ids.txt > '$output'
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
type_cond|names: Enterobacterales type_cond|type_sel: names |
name: value |
value |
| Test-2 |
type_cond|ids: 91347 type_cond|type_sel: ids |
name: value |
value |
| Test-3 |
type_cond|names: Enterobacterales,Hominidae type_cond|type_sel: names |
name: value |
value |
| Test-4 |
type_cond|ids: 91347,9604 type_cond|type_sel: ids |
name: value |
value |