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annotate confab.xml @ 4:4c4e812a67a2 draft

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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
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1 <tool id="ctb_confab" name="Conformer calculation" version="0.4">
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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="2.4.1">openbabel</requirement>
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6 </requirements>
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7 <command detect_errors="aggressive">
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8 <![CDATA[
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10 obabel
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11 '${infile}'
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12 -O '${outfile}'
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13 -i ${infile.ext}
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14 -o sdf
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15 --confab
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16 --rcutoff $RMSD
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17 --ecutoff $energy
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18 --conf $conformers
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19 $first_conformer
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20
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21 ]]>
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22 </command>
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23 <inputs>
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24 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
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25 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
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26 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
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27 <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
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28 <param name='first_conformer' type='boolean' truevalue='--original' falsevalue=''
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29 label='Include the input conformation as the first conformer' />
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30 </inputs>
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31 <outputs>
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32 <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="infile" value='CID_3033.sdf' ftype='sdf' />
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37 <param name='RMSD' value='0.5' />
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38 <param name='energy' value='50.0' />
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39 <param name='conformers' value='10' />
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40 <param name='first_conformer' value="True" />
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41 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="2"/>
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42 </test>
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43 </tests>
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44 <help>
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45 <![CDATA[
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46
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47 .. class:: infomark
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48
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49 **What this tool does**
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50
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51 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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52
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53 .. _Confab: https://code.google.com/p/confab/
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54
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55 -----
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56
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57 .. class:: infomark
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58
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59 **Input**
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60
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61 * Example::
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62
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63 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
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64 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
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65 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
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66 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
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67 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
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68 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
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69 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
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70
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71 .......
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72
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73 1 2 1 0 0 0 0
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74 1 11 1 0 0 0 0
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75 2 3 1 0 0 0 0
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76 3 4 2 0 0 0 0
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77 3 5 1 0 0 0 0
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78 5 6 2 0 0 0 0
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79 6 7 1 0 0 0 0
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80
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81 RMSD cutoff (in Angstrom) 0.5
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82 Energy cutoff (in kcal/mol) 50.0
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83 Max number of conformers to test 100000
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84 Include the input conformation as the first conformer False
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85
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86 -----
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87
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88 .. class:: infomark
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89
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90 **Output**
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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91
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92 * Example::
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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93
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bgruening
parents:
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94 23 26 0 0 0 0 0 0 0 0999 V2000
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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95 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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96 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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97 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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98 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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99 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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100 23.4530 8.7270 62.7850 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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101 24.6970 8.4430 61.9510 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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102 24.4490 8.6370 60.4430 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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103 23.7890 9.9970 60.0980 C 0 0 2 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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104 22.4340 10.0950 60.8720 C 0 0 1 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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105 22.6140 10.0230 62.4340 C 0 0 1 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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106 21.6330 11.3540 60.4500 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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107 21.4320 11.4340 58.9110 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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108 22.7860 11.4040 58.1690 C 0 0 1 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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109 23.4830 10.0600 58.5980 C 0 0 1 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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110 24.6740 9.9180 57.6180 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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111 24.0720 10.4500 56.2670 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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112 22.7140 11.1490 56.6270 C 0 0 2 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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113 23.6590 12.6770 58.4540 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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114 23.4270 11.2460 63.0070 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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115 22.3750 12.3880 55.7810 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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parents:
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116 23.2120 12.8760 55.0520 O 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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117 21.0090 12.9760 55.8570 C 0 0 0 0 0 0 0 0 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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118
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119 ::
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120
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121 1 2 1 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
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122 1 11 1 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
bgruening
parents:
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123 2 3 1 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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124 3 4 2 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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125 3 5 1 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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126 5 6 2 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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127 6 7 1 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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128 6 11 1 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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129 7 8 1 0 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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130 9 8 1 6 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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131 10 9 1 1 0 0 0
039ef13e3676 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
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132
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133
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134
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135 ]]>
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136 </help>
4
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137 <citations>
4c4e812a67a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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138 <citation type="doi">10.1186/1758-2946-3-33</citation>
4c4e812a67a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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139 <citation type="doi">10.1186/1758-2946-3-8</citation>
4c4e812a67a2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
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140 </citations>
3
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141 </tool>