Mercurial > repos > bgruening > confab
changeset 4:4c4e812a67a2 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
| author | bgruening |
|---|---|
| date | Sat, 20 May 2017 08:31:56 -0400 |
| parents | 039ef13e3676 |
| children | 119b462f0f69 |
| files | confab.tar.bz2 confab.xml repository_dependencies.xml test-data/confab_on_CID3033.sdf test-data/confab_on_CID_3033.sdf tool_dependencies.xml |
| diffstat | 6 files changed, 292 insertions(+), 327 deletions(-) [+] |
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--- a/confab.xml Sun Nov 01 10:34:34 2015 -0500 +++ b/confab.xml Sat May 20 08:31:56 2017 -0400 @@ -1,20 +1,23 @@ -<tool id="ctb_confab" name="Conformer calculation" version="0.1"> +<tool id="ctb_confab" name="Conformer calculation" version="0.4"> <description>for molecules (confab)</description> - <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism> + <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism--> <requirements> - <requirement type="package" version="1.0.1">confab</requirement> + <requirement type="package" version="2.4.1">openbabel</requirement> </requirements> - <command> + <command detect_errors="aggressive"> <![CDATA[ - confab + + obabel + '${infile}' + -O '${outfile}' -i ${infile.ext} -o sdf - -r $RMSD - -e $energy - -c $conformers + --confab + --rcutoff $RMSD + --ecutoff $energy + --conf $conformers $first_conformer - $infile - $outfile 2>&1 + ]]> </command> <inputs> @@ -22,7 +25,8 @@ <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' /> <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' /> <param name='conformers' type='integer' value='100' label='Max number of conformers to test' /> - <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' /> + <param name='first_conformer' type='boolean' truevalue='--original' falsevalue='' + label='Include the input conformation as the first conformer' /> </inputs> <outputs> <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/> @@ -32,9 +36,9 @@ <param name="infile" value='CID_3033.sdf' ftype='sdf' /> <param name='RMSD' value='0.5' /> <param name='energy' value='50.0' /> - <param name='conformers' value='100000' /> - <param name='first_conformer' value='-a' /> - <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' /> + <param name='conformers' value='10' /> + <param name='first_conformer' value="True" /> + <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="2"/> </test> </tests> <help> @@ -126,17 +130,12 @@ 9 8 1 6 0 0 0 10 9 1 1 0 0 0 ------ - -.. class:: infomark - -**Cite** - -Confab_ - -.. _Confab: https://code.google.com/p/confab/ ]]> </help> + <citations> + <citation type="doi">10.1186/1758-2946-3-33</citation> + <citation type="doi">10.1186/1758-2946-3-8</citation> + </citations> </tool>
--- a/repository_dependencies.xml Sun Nov 01 10:34:34 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> - <repository changeset_revision="85eca06eefc6" name="molecule_datatypes" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> -</repositories>
--- a/test-data/confab_on_CID3033.sdf Sun Nov 01 10:34:34 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,270 +0,0 @@ -214.7 - OpenBabel06291213403D - - 30 31 0 0 0 0 0 0 0 0999 V2000 - 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 - -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 - -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 - 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 - -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 - -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 - -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 - 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 - -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 - -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 - -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 - -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 - 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 - -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 - 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 - 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 - -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 - -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 - -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 - -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 - 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 - -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 - -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 - 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 - 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 - 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 - -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 - 1 14 1 0 0 0 0 - 2 15 1 0 0 0 0 - 3 16 1 0 0 0 0 - 3 30 1 0 0 0 0 - 4 16 2 0 0 0 0 - 5 7 1 0 0 0 0 - 5 9 1 0 0 0 0 - 5 22 1 0 0 0 0 - 6 7 1 0 0 0 0 - 6 8 1 0 0 0 0 - 6 10 2 0 0 0 0 - 7 11 2 0 0 0 0 - 8 16 1 0 0 0 0 - 8 20 1 0 0 0 0 - 8 21 1 0 0 0 0 - 9 14 2 0 0 0 0 - 9 15 1 0 0 0 0 - 10 12 1 0 0 0 0 - 10 23 1 0 0 0 0 - 11 13 1 0 0 0 0 - 11 24 1 0 0 0 0 - 12 13 2 0 0 0 0 - 12 25 1 0 0 0 0 - 13 26 1 0 0 0 0 - 14 17 1 0 0 0 0 - 15 18 2 0 0 0 0 - 17 19 2 0 0 0 0 - 17 27 1 0 0 0 0 - 18 19 1 0 0 0 0 - 18 28 1 0 0 0 0 - 19 29 1 0 0 0 0 -M END -> <PUBCHEM_COMPOUND_CID> -3033 - -> <PUBCHEM_CONFORMER_RMSD> -0.6 - -> <PUBCHEM_CONFORMER_DIVERSEORDER> -1 -20 -18 -39 -29 -42 -38 -35 -30 -25 -33 -28 -32 -36 -26 -24 -40 -11 -27 -37 -7 -41 -10 -19 -43 -8 -6 -16 -44 -23 -34 -14 -15 -31 -9 -13 -17 -21 -22 -5 -12 -2 -3 -4 - -> <PUBCHEM_MMFF94_PARTIAL_CHARGES> -28 -1 -0.18 -10 -0.15 -11 -0.15 -12 -0.15 -13 -0.15 -14 0.18 -15 0.18 -16 0.66 -17 -0.15 -18 -0.15 -19 -0.15 -2 -0.18 -22 0.4 -23 0.15 -24 0.15 -25 0.15 -26 0.15 -27 0.15 -28 0.15 -29 0.15 -3 -0.65 -30 0.5 -4 -0.57 -5 -0.6 -6 -0.14 -7 0.1 -8 0.2 -9 0.1 - -> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> -4 - -> <PUBCHEM_PHARMACOPHORE_FEATURES> -7 -1 3 acceptor -1 4 acceptor -1 5 cation -1 5 donor -3 3 4 16 anion -6 6 7 10 11 12 13 rings -6 9 14 15 17 18 19 rings - -> <PUBCHEM_HEAVY_ATOM_COUNT> -19 - -> <PUBCHEM_ATOM_DEF_STEREO_COUNT> -0 - -> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> -0 - -> <PUBCHEM_BOND_DEF_STEREO_COUNT> -0 - -> <PUBCHEM_BOND_UDEF_STEREO_COUNT> -0 - -> <PUBCHEM_ISOTOPIC_ATOM_COUNT> -0 - -> <PUBCHEM_COMPONENT_COUNT> -1 - -> <PUBCHEM_CACTVS_TAUTO_COUNT> -1 - -> <PUBCHEM_CONFORMER_ID> -00000BD900000001 - -> <PUBCHEM_MMFF94_ENERGY> -65.6362 - -> <PUBCHEM_FEATURE_SELFOVERLAP> -35.578 - -> <PUBCHEM_SHAPE_FINGERPRINT> -10366900 7 17386020514759110480 -114674 6 16903282898360328323 -11578080 2 17913245089295617604 -11582403 64 14544541357940910356 -11640471 11 18127963303313961600 -12236239 1 18272088352834916308 -12363563 72 18042978579496277287 -12553582 1 18190740839094073615 -12596599 1 18201439237582433270 -12788726 201 18410285909464206003 -13032168 30 18201440238019390274 -13140716 1 18187086113919468457 -13538477 17 18339642338307470464 -13583140 156 17241914119188522922 -13764800 53 17895191172601517065 -13965767 371 17259888045752176376 -14115302 16 18342181093776810149 -14787075 74 17907866106787333628 -15279307 12 18198622322777022915 -15375462 189 18270674264943931347 -15669948 3 18336550511731321249 -16752209 62 18336841852664817743 -16945 1 18188484791351783177 -19433438 48 18059583550169763352 -200 152 18130792217719576158 -20645476 183 18270115859187436189 -20905425 154 17970632883131290416 -21452121 199 18046637711133085653 -21639500 275 16988270998321974524 -22112679 90 18342446063036096292 -23419403 2 17835564502519425292 -23493267 7 18115023138028600728 -23526113 38 16660924516543134566 -23557571 272 17821721762863303772 -23559900 14 17896315990920094510 -23598288 3 18411412925846384519 -23598291 2 18059009613384180254 -238 59 16343141308025475526 -4340502 62 17273677940604857177 -6049 1 17240202131864233360 -6992083 37 18058168521433072460 -7615 1 18201433675414973908 -77492 1 18272651289913926852 -81228 2 17968373550240022809 -9709674 26 17896035610527288590 - -> <PUBCHEM_SHAPE_MULTIPOLES> -378.03 -7.01 -2.75 -1.77 -0.78 -1.58 -0.3 -0.41 -1.94 --1.08 -1.9 --8.69 -11.04 -2.58 - -> <PUBCHEM_SHAPE_SELFOVERLAP> -790.335 - -> <PUBCHEM_SHAPE_VOLUME> -214.7 - -> <PUBCHEM_COORDINATE_TYPE> -2 -5 -255 - -$$$$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/confab_on_CID_3033.sdf Sat May 20 08:31:56 2017 -0400 @@ -0,0 +1,270 @@ +3033 + OpenBabel05191717063D + + 30 31 0 0 0 0 0 0 0 0999 V2000 + 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1377 -1.6392 2.1136 Cl 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2620 -2.9284 -1.0647 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7906 -1.9108 0.9092 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2679 -0.2051 -0.3990 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0640 0.5139 -0.3769 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7313 0.7178 -0.0192 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4761 -0.6830 -1.1703 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6571 -0.2482 -0.1795 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0382 1.4350 0.0081 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3728 1.8429 0.7234 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6797 2.5600 0.7506 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3470 2.7640 1.1083 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5353 0.3477 -1.0918 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1740 -0.8865 0.9534 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8480 -1.8749 -0.3123 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9124 0.3058 -0.8739 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5511 -0.9285 1.1713 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.4203 -0.3324 0.2576 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7086 -0.9792 -1.8930 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3614 -0.4266 -1.7676 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0861 -1.1146 -0.6780 H 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0812 1.2885 -0.2604 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6569 2.0278 1.0167 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4382 3.2769 1.0511 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0683 3.6399 1.6868 H 0 0 0 0 0 0 0 0 0 0 0 0 + 4.6037 0.7654 -1.5758 H 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9635 -1.4215 2.0480 H 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4925 -0.3651 0.4274 H 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5025 -3.7011 -0.5102 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 14 1 0 0 0 0 + 2 15 1 0 0 0 0 + 3 16 1 0 0 0 0 + 3 30 1 0 0 0 0 + 4 16 2 0 0 0 0 + 5 7 1 0 0 0 0 + 5 9 1 0 0 0 0 + 5 22 1 0 0 0 0 + 6 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + 6 10 2 0 0 0 0 + 7 11 2 0 0 0 0 + 8 16 1 0 0 0 0 + 8 20 1 0 0 0 0 + 8 21 1 0 0 0 0 + 9 14 2 0 0 0 0 + 9 15 1 0 0 0 0 + 10 12 1 0 0 0 0 + 10 23 1 0 0 0 0 + 11 13 1 0 0 0 0 + 11 24 1 0 0 0 0 + 12 13 2 0 0 0 0 + 12 25 1 0 0 0 0 + 13 26 1 0 0 0 0 + 14 17 1 0 0 0 0 + 15 18 2 0 0 0 0 + 17 19 2 0 0 0 0 + 17 27 1 0 0 0 0 + 18 19 1 0 0 0 0 + 18 28 1 0 0 0 0 + 19 29 1 0 0 0 0 +M END +> <PUBCHEM_COMPOUND_CID> +3033 + +> <PUBCHEM_CONFORMER_RMSD> +0.6 + +> <PUBCHEM_CONFORMER_DIVERSEORDER> +1 +20 +18 +39 +29 +42 +38 +35 +30 +25 +33 +28 +32 +36 +26 +24 +40 +11 +27 +37 +7 +41 +10 +19 +43 +8 +6 +16 +44 +23 +34 +14 +15 +31 +9 +13 +17 +21 +22 +5 +12 +2 +3 +4 + +> <PUBCHEM_MMFF94_PARTIAL_CHARGES> +28 +1 -0.18 +10 -0.15 +11 -0.15 +12 -0.15 +13 -0.15 +14 0.18 +15 0.18 +16 0.66 +17 -0.15 +18 -0.15 +19 -0.15 +2 -0.18 +22 0.4 +23 0.15 +24 0.15 +25 0.15 +26 0.15 +27 0.15 +28 0.15 +29 0.15 +3 -0.65 +30 0.5 +4 -0.57 +5 -0.6 +6 -0.14 +7 0.1 +8 0.2 +9 0.1 + +> <PUBCHEM_EFFECTIVE_ROTOR_COUNT> +4 + +> <PUBCHEM_PHARMACOPHORE_FEATURES> +7 +1 3 acceptor +1 4 acceptor +1 5 cation +1 5 donor +3 3 4 16 anion +6 6 7 10 11 12 13 rings +6 9 14 15 17 18 19 rings + +> <PUBCHEM_HEAVY_ATOM_COUNT> +19 + +> <PUBCHEM_ATOM_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_ATOM_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_DEF_STEREO_COUNT> +0 + +> <PUBCHEM_BOND_UDEF_STEREO_COUNT> +0 + +> <PUBCHEM_ISOTOPIC_ATOM_COUNT> +0 + +> <PUBCHEM_COMPONENT_COUNT> +1 + +> <PUBCHEM_CACTVS_TAUTO_COUNT> +1 + +> <PUBCHEM_CONFORMER_ID> +00000BD900000001 + +> <PUBCHEM_MMFF94_ENERGY> +65.6362 + +> <PUBCHEM_FEATURE_SELFOVERLAP> +35.578 + +> <PUBCHEM_SHAPE_FINGERPRINT> +10366900 7 17386020514759110480 +114674 6 16903282898360328323 +11578080 2 17913245089295617604 +11582403 64 14544541357940910356 +11640471 11 18127963303313961600 +12236239 1 18272088352834916308 +12363563 72 18042978579496277287 +12553582 1 18190740839094073615 +12596599 1 18201439237582433270 +12788726 201 18410285909464206003 +13032168 30 18201440238019390274 +13140716 1 18187086113919468457 +13538477 17 18339642338307470464 +13583140 156 17241914119188522922 +13764800 53 17895191172601517065 +13965767 371 17259888045752176376 +14115302 16 18342181093776810149 +14787075 74 17907866106787333628 +15279307 12 18198622322777022915 +15375462 189 18270674264943931347 +15669948 3 18336550511731321249 +16752209 62 18336841852664817743 +16945 1 18188484791351783177 +19433438 48 18059583550169763352 +200 152 18130792217719576158 +20645476 183 18270115859187436189 +20905425 154 17970632883131290416 +21452121 199 18046637711133085653 +21639500 275 16988270998321974524 +22112679 90 18342446063036096292 +23419403 2 17835564502519425292 +23493267 7 18115023138028600728 +23526113 38 16660924516543134566 +23557571 272 17821721762863303772 +23559900 14 17896315990920094510 +23598288 3 18411412925846384519 +23598291 2 18059009613384180254 +238 59 16343141308025475526 +4340502 62 17273677940604857177 +6049 1 17240202131864233360 +6992083 37 18058168521433072460 +7615 1 18201433675414973908 +77492 1 18272651289913926852 +81228 2 17968373550240022809 +9709674 26 17896035610527288590 + +> <PUBCHEM_SHAPE_MULTIPOLES> +378.03 +7.01 +2.75 +1.77 +0.78 +1.58 +0.3 +0.41 +1.94 +-1.08 +1.9 +-8.69 +11.04 +2.58 + +> <PUBCHEM_SHAPE_SELFOVERLAP> +790.335 + +> <PUBCHEM_SHAPE_VOLUME> +214.7 + +> <PUBCHEM_COORDINATE_TYPE> +2 +5 +255 + +$$$$
--- a/tool_dependencies.xml Sun Nov 01 10:34:34 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="eigen2" version="2.0.17"> - <repository changeset_revision="a270fba04f3a" name="package_eigen_2_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="confab" version="1.0.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://github.com/bgruening/confab/archive/1.0.1.tar.gz</action> - - <!-- populate the environment variables from the dependend repos --> - <action type="set_environment_for_install"> - <repository changeset_revision="a270fba04f3a" name="package_eigen_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> - <package name="eigen2" version="2.0.17" /> - </repository> - </action> - - <action type="shell_command">cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN2_INCLUDE_DIR=$EIGEN2_SOURCE_PATH</action> - <action type="shell_command">make</action> - <action type="shell_command">make install</action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="set_to" name="BABEL_DATADIR">$INSTALL_DIR/share/openbabel</environment_variable> - <environment_variable action="set_to" name="BABEL_LIBDIR">$INSTALL_DIR/lib/openbabel/2.2.99</environment_variable> - </action> - </actions> - </install> - <readme>Compiling Confab requires g++, CMake 2.4+. Optional but required for a few features is libxml2 and zlib.</readme> - </package> -</tool_dependency>