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annotate confab.xml @ 21:ff23947232d0 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 10:29:42 -0500
parents a396884f933a
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1 <tool id="ctb_confab" name="Conformer calculation" version="0.1">
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2 <description>for molecules (confab)</description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="1.0.1">confab</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 confab
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10 -i ${infile.ext}
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11 -o sdf
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12 -r $RMSD
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13 -e $energy
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14 -c $conformers
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15 $first_conformer
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16 $infile
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17 $outfile 2>&1
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
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22 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
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23 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
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24 <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
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25 <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' />
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26 </inputs>
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27 <outputs>
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28 <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="infile" value='CID_3033.sdf' ftype='sdf' />
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33 <param name='RMSD' value='0.5' />
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34 <param name='energy' value='50.0' />
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35 <param name='conformers' value='100000' />
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36 <param name='first_conformer' value='-a' />
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37 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
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38 </test>
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39 </tests>
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40 <help>
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41 <![CDATA[
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43 .. class:: infomark
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45 **What this tool does**
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46
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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.
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48
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49 .. _Confab: https://code.google.com/p/confab/
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50
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51 -----
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53 .. class:: infomark
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55 **Input**
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56
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57 * Example::
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59 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
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60 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
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61 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
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62 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
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63 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
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64 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
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65 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
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67 .......
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69 1 2 1 0 0 0 0
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70 1 11 1 0 0 0 0
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71 2 3 1 0 0 0 0
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72 3 4 2 0 0 0 0
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73 3 5 1 0 0 0 0
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74 5 6 2 0 0 0 0
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75 6 7 1 0 0 0 0
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77 RMSD cutoff (in Angstrom) 0.5
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78 Energy cutoff (in kcal/mol) 50.0
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79 Max number of conformers to test 100000
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80 Include the input conformation as the first conformer False
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82 -----
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83
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84 .. class:: infomark
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85
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86 **Output**
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87
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88 * Example::
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90 23 26 0 0 0 0 0 0 0 0999 V2000
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91 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
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92 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
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93 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
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94 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
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95 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
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96 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
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97 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
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98 24.4490 8.6370 60.4430 C 0 0 0 0 0 0 0 0 0 0 0 0
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99 23.7890 9.9970 60.0980 C 0 0 2 0 0 0 0 0 0 0 0 0
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100 22.4340 10.0950 60.8720 C 0 0 1 0 0 0 0 0 0 0 0 0
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101 22.6140 10.0230 62.4340 C 0 0 1 0 0 0 0 0 0 0 0 0
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102 21.6330 11.3540 60.4500 C 0 0 0 0 0 0 0 0 0 0 0 0
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103 21.4320 11.4340 58.9110 C 0 0 0 0 0 0 0 0 0 0 0 0
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104 22.7860 11.4040 58.1690 C 0 0 1 0 0 0 0 0 0 0 0 0
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105 23.4830 10.0600 58.5980 C 0 0 1 0 0 0 0 0 0 0 0 0
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106 24.6740 9.9180 57.6180 C 0 0 0 0 0 0 0 0 0 0 0 0
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107 24.0720 10.4500 56.2670 C 0 0 0 0 0 0 0 0 0 0 0 0
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108 22.7140 11.1490 56.6270 C 0 0 2 0 0 0 0 0 0 0 0 0
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109 23.6590 12.6770 58.4540 C 0 0 0 0 0 0 0 0 0 0 0 0
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110 23.4270 11.2460 63.0070 C 0 0 0 0 0 0 0 0 0 0 0 0
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111 22.3750 12.3880 55.7810 C 0 0 0 0 0 0 0 0 0 0 0 0
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112 23.2120 12.8760 55.0520 O 0 0 0 0 0 0 0 0 0 0 0 0
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113 21.0090 12.9760 55.8570 C 0 0 0 0 0 0 0 0 0 0 0 0
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115 ::
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117 1 2 1 0 0 0 0
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118 1 11 1 0 0 0 0
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119 2 3 1 0 0 0 0
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120 3 4 2 0 0 0 0
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121 3 5 1 0 0 0 0
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122 5 6 2 0 0 0 0
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123 6 7 1 0 0 0 0
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124 6 11 1 0 0 0 0
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125 7 8 1 0 0 0 0
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126 9 8 1 6 0 0 0
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127 10 9 1 1 0 0 0
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129 -----
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131 .. class:: infomark
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132
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133 **Cite**
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134
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135 Confab_
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136
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137 .. _Confab: https://code.google.com/p/confab/
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140 ]]>
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141 </help>
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142 </tool>