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comparison confab.xml @ 3:039ef13e3676 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
author bgruening
date Sun, 01 Nov 2015 10:34:34 -0500
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2:548537fc2577 3:039ef13e3676
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>
7 <command>
8 <![CDATA[
9 confab
10 -i ${infile.ext}
11 -o sdf
12 -r $RMSD
13 -e $energy
14 -c $conformers
15 $first_conformer
16 $infile
17 $outfile 2>&1
18 ]]>
19 </command>
20 <inputs>
21 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
22 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
23 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
24 <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
25 <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' />
26 </inputs>
27 <outputs>
28 <data format="sdf" name="outfile" label="${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' />
38 </test>
39 </tests>
40 <help>
41 <![CDATA[
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::
58
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
140 ]]>
141 </help>
142 </tool>