Repository revision
13:274193d6c443

Repository 'openbabel_obgrep'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_obgrep

Compound search tool metadata
Miscellaneous
- an advanced molecular search program using SMARTS
openbabel_obgrep
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_obgrep/openbabel_obgrep/3.1.1+galaxy0
3.1.1+galaxy0
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_obgrep/openbabel_obgrep/3.1.1+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_obgrep/openbabel_obgrep/2.4.2.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_obgrep/openbabel_obgrep/2.4.2.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_obgrep/openbabel_obgrep/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_obgrep/openbabel_obgrep/2.4.1.0
openbabel_obgrep
Requirements (dependencies defined in the <requirements> tag set)
name version type
openbabel 3.1.1 package
python 3.6 package
Additional information about this tool
#if $input_type.inp == 'single':
            obgrep
                $invert_matches
                #if $n_times:
                    -t $n_times
                #end if
                $only_name
                $full_match
                $number_of_matches
                -i '${infile.ext}'
                '${input_type.smarts_pattern}'
                '${infile}'
                > '${outfile}'
        #else if $input_type.inp == 'multi':
            python '$__tool_directory__/multi_obgrep.py'
                -i $infile
                --iformat ${infile.ext}
                -q '${input_type.query}'
                -o '${outfile}'
                $invert_matches
                --n-times $n_times
                $only_name
                $full_match
                $number_of_matches
                --processors "\${GALAXY_SLOTS:-12}"
        #end if


    
None
False
Functional tests
name inputs outputs required files
Test-1 infile: 8_mol.smi
input_type|smarts_pattern: CO
input_type|inp: single
invert_matches: False
only_name: False
full_match: False
number_of_matches: False
name: value
8_mol.smi
value
Test-2 infile: 2_mol.smi
input_type|query: pattern.smarts
input_type|inp: multi
name: value
2_mol.smi
pattern.smarts
value