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1 <tool id="chemfp_ob2fps" name="Molecules to Fingerprints" version="0.1.2">
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2 <description>with different fingerprint types</description>
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3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="outfile"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="1.1p1">chemfp</requirement>
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6 </requirements>
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7 <command>
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8 ob2fps $fptype --in "${infile.ext}" "${infile}" -o "${outfile}" --errors report 2>&1
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9 </command>
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10 <inputs>
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11 <param name="infile" type='data' format="sdf,smi,mol,mol2,cml,inchi" label="molecule file"/>
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12 <param name='fptype' type='select' format='text'>
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13 <option value='--FP2'>FP2</option>
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14 <option value='--FP3'>FP3</option>
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15 <option value='--FP4'>FP4</option>
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16 <option value='--MACCS'>MACCS</option>
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17 </param>
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18 </inputs>
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19 <outputs>
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20 <data name="outfile" format="fps" />
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21 </outputs>
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22 <tests>
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23 <!-- FP2 -->
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24 <test>
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25 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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26 <param name="fptype" value="--FP2" />
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27 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
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28 </test>
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29 <test>
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30 <param name="infile" value="CID_2244.smi" ftype="smi" />
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31 <param name="fptype" value="--FP2" />
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32 <output name="outfile" file="CID_2244_FP2.fps" ftype="fps" />
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33 </test>
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34 <!-- FP3 -->
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35 <test>
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36 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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37 <param name="fptype" value="--FP3" />
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38 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
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39 </test>
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40 <test>
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41 <param name="infile" value="CID_2244.smi" ftype="smi" />
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42 <param name="fptype" value="--FP3" />
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43 <output name="outfile" file="CID_2244_FP3.fps" ftype="fps" />
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44 </test>
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45 <!-- FP4 -->
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46 <test>
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47 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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48 <param name="fptype" value="--FP4" />
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49 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
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50 </test>
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51 <test>
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52 <param name="infile" value="CID_2244.smi" ftype="smi" />
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53 <param name="fptype" value="--FP4" />
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54 <output name="outfile" file="CID_2244_FP4.fps" ftype="fps" />
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55 </test>
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56 <!-- MACCS -->
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57 <test>
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58 <param name="infile" value="CID_2244.sdf" ftype="sdf" />
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59 <param name="fptype" value="--MACCS" />
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60 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
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61 </test>
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62 <test>
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63 <param name="infile" value="CID_2244.smi" ftype="smi" />
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64 <param name="fptype" value="--MACCS" />
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65 <output name="outfile" file="CID_2244_MACCS.fps" ftype="fps" />
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66 </test>
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67 </tests>
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68 <help>
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69
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70
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71 **What it does**
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72
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73 Generate fingerprints using OpenBabel
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74
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75 -----
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76
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77 **Example**
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78
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79 * input::
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80
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81 - SDF File
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82
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83 28434379
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84 -OEChem-02031205132D
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85
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86 37 39 0 0 0 0 0 0 0999 V2000
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87 8.1648 -1.8842 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
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88 6.0812 -0.2134 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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89 6.0812 -1.8229 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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90 2.5369 -2.0182 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
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91 6.3919 0.7371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
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92 7.3704 0.9433 0.0000 C 0 0 0 0
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93 ......
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94 1 15 1 0 0 0 0
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95 1 35 1 0 0 0 0
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96 2 5 1 0 0 0 0
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97 2 11 1 0 0 0 0
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98 2 12 1 0 0 0 0
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99 3 12 2 0 0 0 0
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100 3 13 1 0 0 0 0
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101 4 18 1 0 0 0 0
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102 ......
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103
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104 >PUBCHEM_COMPOUND_CID<
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105 28434379
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106
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107 > <PUBCHEM_COMPOUND_CANONICALIZED>
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108 1
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109
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110 > <PUBCHEM_CACTVS_COMPLEXITY>
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111 280
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112
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113 > <PUBCHEM_CACTVS_HBOND_ACCEPTOR>
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114 2
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115
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116 > <PUBCHEM_CACTVS_HBOND_DONOR>
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117 2
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118
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119 > <PUBCHEM_CACTVS_ROTATABLE_BOND>
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120 2
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121
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122 > <PUBCHEM_CACTVS_SUBSKEYS>
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123 AAADceBzIAAAAAAAAAAAAAAAAAAAAWAAAAAwYAAAAAAAAFgB8AAAHgAQCAAACCjhlwYx0LdMEgCgASZiZASCgC0hEqAJ2CA4dJiKeKLA2dGUJAhokALYyCcQAAAAAACAAAQAACAAAQAACAAAQAAAAAAAAA==
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124
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125 >
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126
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127 - type : FP2
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128
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129 * output::
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130
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131 #FPS1
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132 #num_bits=1021
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133 #type=OpenBabel-FP2/1
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134 #software=OpenBabel/2.3.0
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135 #source=/tmp/dataset_409.dat.sdf
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136 #date=2012-02-03T11:13:39
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137 c0000000000008c0000846000400000000000010800000000000004000000000100010000700802170000018000000c
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138 0010000000020600208008000008000000c000c02c00002000000c00000100000008001400c800001c0180000000300
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139 10000000000080000000c0000060000c0000060810000010000000800102000000 28434379
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140
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141
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142 </help>
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143 </tool>
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