Mercurial > repos > bgruening > confab
annotate confab.xml @ 1:731ad135ddb4 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
| author | bgruening |
|---|---|
| date | Sun, 01 Nov 2015 10:28:54 -0500 |
| parents | 4a73b5059c22 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="ctb_confab" name="Conformer calculation" version="0.1"> |
| 2 <description>for molecules (confab)</description> | |
| 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="1.0.1">confab</requirement> | |
| 6 </requirements> | |
|
1
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
7 <command> |
|
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
8 <![CDATA[ |
|
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
9 confab |
| 0 | 10 -i ${infile.ext} |
| 11 -o sdf | |
|
1
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
12 -r $RMSD |
|
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
13 -e $energy |
|
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
14 -c $conformers |
|
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
15 $first_conformer |
| 0 | 16 $infile |
|
1
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
17 $outfile 2>&1 |
|
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
18 ]]> |
| 0 | 19 </command> |
| 20 <inputs> | |
| 21 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/> | |
| 22 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' /> | |
| 23 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' /> | |
| 24 <param name='conformers' type='integer' value='100' label='Max number of conformers to test' /> | |
| 25 <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' /> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/> | |
| 29 </outputs> | |
| 30 <tests> | |
| 31 <test> | |
| 32 <param name="infile" value='CID_3033.sdf' ftype='sdf' /> | |
| 33 <param name='RMSD' value='0.5' /> | |
| 34 <param name='energy' value='50.0' /> | |
| 35 <param name='conformers' value='100000' /> | |
| 36 <param name='first_conformer' value='-a' /> | |
| 37 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' /> | |
|
1
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
38 </test> |
| 0 | 39 </tests> |
| 40 <help> | |
|
1
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
41 <![CDATA[ |
| 0 | 42 |
| 43 .. class:: infomark | |
| 44 | |
| 45 **What this tool does** | |
| 46 | |
| 47 Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialisation steps, is used to generate multiple conformers which are filtered on-the-fly to identify diverse low energy conformers. | |
| 48 | |
| 49 .. _Confab: https://code.google.com/p/confab/ | |
| 50 | |
| 51 ----- | |
| 52 | |
| 53 .. class:: infomark | |
| 54 | |
| 55 **Input** | |
| 56 | |
| 57 * Example:: | |
|
1
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
58 |
| 0 | 59 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 |
| 60 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 61 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 62 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 63 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 64 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 65 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 66 | |
| 67 ....... | |
| 68 | |
| 69 1 2 1 0 0 0 0 | |
| 70 1 11 1 0 0 0 0 | |
| 71 2 3 1 0 0 0 0 | |
| 72 3 4 2 0 0 0 0 | |
| 73 3 5 1 0 0 0 0 | |
| 74 5 6 2 0 0 0 0 | |
| 75 6 7 1 0 0 0 0 | |
| 76 | |
| 77 RMSD cutoff (in Angstrom) 0.5 | |
| 78 Energy cutoff (in kcal/mol) 50.0 | |
| 79 Max number of conformers to test 100000 | |
| 80 Include the input conformation as the first conformer False | |
| 81 | |
| 82 ----- | |
| 83 | |
| 84 .. class:: infomark | |
| 85 | |
| 86 **Output** | |
| 87 | |
| 88 * Example:: | |
| 89 | |
| 90 23 26 0 0 0 0 0 0 0 0999 V2000 | |
| 91 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 92 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 93 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 94 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 95 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 96 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 97 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 98 24.4490 8.6370 60.4430 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 99 23.7890 9.9970 60.0980 C 0 0 2 0 0 0 0 0 0 0 0 0 | |
| 100 22.4340 10.0950 60.8720 C 0 0 1 0 0 0 0 0 0 0 0 0 | |
| 101 22.6140 10.0230 62.4340 C 0 0 1 0 0 0 0 0 0 0 0 0 | |
| 102 21.6330 11.3540 60.4500 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 103 21.4320 11.4340 58.9110 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 104 22.7860 11.4040 58.1690 C 0 0 1 0 0 0 0 0 0 0 0 0 | |
| 105 23.4830 10.0600 58.5980 C 0 0 1 0 0 0 0 0 0 0 0 0 | |
| 106 24.6740 9.9180 57.6180 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 107 24.0720 10.4500 56.2670 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 108 22.7140 11.1490 56.6270 C 0 0 2 0 0 0 0 0 0 0 0 0 | |
| 109 23.6590 12.6770 58.4540 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 110 23.4270 11.2460 63.0070 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 111 22.3750 12.3880 55.7810 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 112 23.2120 12.8760 55.0520 O 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 113 21.0090 12.9760 55.8570 C 0 0 0 0 0 0 0 0 0 0 0 0 | |
| 114 | |
| 115 :: | |
| 116 | |
| 117 1 2 1 0 0 0 0 | |
| 118 1 11 1 0 0 0 0 | |
| 119 2 3 1 0 0 0 0 | |
| 120 3 4 2 0 0 0 0 | |
| 121 3 5 1 0 0 0 0 | |
| 122 5 6 2 0 0 0 0 | |
| 123 6 7 1 0 0 0 0 | |
| 124 6 11 1 0 0 0 0 | |
| 125 7 8 1 0 0 0 0 | |
| 126 9 8 1 6 0 0 0 | |
| 127 10 9 1 1 0 0 0 | |
| 128 | |
| 129 ----- | |
| 130 | |
| 131 .. class:: infomark | |
| 132 | |
| 133 **Cite** | |
| 134 | |
| 135 Confab_ | |
| 136 | |
| 137 .. _Confab: https://code.google.com/p/confab/ | |
| 138 | |
| 139 | |
|
1
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
140 ]]> |
|
731ad135ddb4
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
0
diff
changeset
|
141 </help> |
| 0 | 142 </tool> |