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annotate confab.xml @ 28:4bd0cbd904d5 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 11:54:35 +0000
parents 7198475e0755
children
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1 <tool id="ctb_confab" name="Conformer calculation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <macros>
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3 <token name="@TOOL_VERSION@">3.1.1</token>
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4 <token name="@GALAXY_VERSION@">0</token>
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5 </macros>
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6 <description>for molecules (confab) with OpenBabel</description>
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7 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism-->
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8 <requirements>
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9 <requirement type="package" version="@TOOL_VERSION@">openbabel</requirement>
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10 </requirements>
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11 <command detect_errors="aggressive">
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12 <![CDATA[
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14 obabel
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15 '${infile}'
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16 -O '${outfile}'
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17 -i ${infile.ext}
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18 -o sdf
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19 --confab
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20 --verbose
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21 --rcutoff $RMSD
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22 --ecutoff $energy
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23 --conf $conformers
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24 $first_conformer
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25
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26 ]]>
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27 </command>
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28 <inputs>
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29 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates in SDF or MOL2 format" help="Dataset missing? See TIP below"/>
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30 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (Å)' help='Minimum RMSD deviation from the original conformation in order to be classified as a separate conformer.'/>
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31 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' help='Minimum energy difference to the original conformation in order to be classified as a separate conformer.'/>
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32 <param name='conformers' type='integer' value='1000000' label='Max number of conformers to test' />
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33 <param name='first_conformer' type='boolean' truevalue='--original' falsevalue=''
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34 label='Include the input conformation as the first conformer' help='If yes, the original conformation is included in the output file'/>
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35 </inputs>
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36 <outputs>
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37 <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="infile" value='CID_3033.sdf' ftype='sdf' />
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42 <param name='RMSD' value='0.5' />
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43 <param name='energy' value='50.0' />
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44 <param name='conformers' value='10' />
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45 <param name='first_conformer' value="True" />
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46 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="2"/>
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47 </test>
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48 </tests>
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49 <help>
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50 <![CDATA[
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51
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52 .. class:: infomark
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53
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54 **What this tool does**
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55
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56 Confab_ is a conformation generator. The algorithm starts with an input 3D structure which, after some initialization steps, is used to generate multiple conformers, which are filtered on-the-fly to identify diverse low-energy conformers.
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57
27
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58 .. _Confab: https://open-babel.readthedocs.io/en/latest/3DStructureGen/multipleconformers.html#confab
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59
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60 -----
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61
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62 .. class:: infomark
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63
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64 **Input**
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65
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66 * Example::
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67
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68 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
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69 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
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70 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
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71 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
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72 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
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73 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
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74 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
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75
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76 .......
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77
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78 1 2 1 0 0 0 0
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79 1 11 1 0 0 0 0
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80 2 3 1 0 0 0 0
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81 3 4 2 0 0 0 0
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82 3 5 1 0 0 0 0
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83 5 6 2 0 0 0 0
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84 6 7 1 0 0 0 0
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85
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86 RMSD cutoff (in Angstrom) 0.5
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87 Energy cutoff (in kcal/mol) 50.0
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88 Max number of conformers to test 100000
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89 Include the input conformation as the first conformer False
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90
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91 -----
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92
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93 .. class:: infomark
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94
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95 **Output**
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96
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97 * Example::
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98
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99 23 26 0 0 0 0 0 0 0 0999 V2000
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100 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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101 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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102 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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103 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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104 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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105 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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106 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
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107 24.4490 8.6370 60.4430 C 0 0 0 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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108 23.7890 9.9970 60.0980 C 0 0 2 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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109 22.4340 10.0950 60.8720 C 0 0 1 0 0 0 0 0 0 0 0 0
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110 22.6140 10.0230 62.4340 C 0 0 1 0 0 0 0 0 0 0 0 0
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111 21.6330 11.3540 60.4500 C 0 0 0 0 0 0 0 0 0 0 0 0
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112 21.4320 11.4340 58.9110 C 0 0 0 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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113 22.7860 11.4040 58.1690 C 0 0 1 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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114 23.4830 10.0600 58.5980 C 0 0 1 0 0 0 0 0 0 0 0 0
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115 24.6740 9.9180 57.6180 C 0 0 0 0 0 0 0 0 0 0 0 0
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116 24.0720 10.4500 56.2670 C 0 0 0 0 0 0 0 0 0 0 0 0
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117 22.7140 11.1490 56.6270 C 0 0 2 0 0 0 0 0 0 0 0 0
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118 23.6590 12.6770 58.4540 C 0 0 0 0 0 0 0 0 0 0 0 0
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119 23.4270 11.2460 63.0070 C 0 0 0 0 0 0 0 0 0 0 0 0
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120 22.3750 12.3880 55.7810 C 0 0 0 0 0 0 0 0 0 0 0 0
d323837e346d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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121 23.2120 12.8760 55.0520 O 0 0 0 0 0 0 0 0 0 0 0 0
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122 21.0090 12.9760 55.8570 C 0 0 0 0 0 0 0 0 0 0 0 0
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123
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124 ::
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125
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126 1 2 1 0 0 0 0
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127 1 11 1 0 0 0 0
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128 2 3 1 0 0 0 0
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129 3 4 2 0 0 0 0
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130 3 5 1 0 0 0 0
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131 5 6 2 0 0 0 0
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132 6 7 1 0 0 0 0
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133 6 11 1 0 0 0 0
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134 7 8 1 0 0 0 0
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135 9 8 1 6 0 0 0
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136 10 9 1 1 0 0 0
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137
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138
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139
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140 ]]>
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141 </help>
24
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142 <citations>
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143 <citation type="doi">10.1186/1758-2946-3-33</citation>
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144 <citation type="doi">10.1186/1758-2946-3-8</citation>
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145 </citations>
23
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146 </tool>