Mercurial > repos > jay > pdaug_sequence_property_based_descriptors
annotate PDAUG_Sequence_Property_Based_Descriptors/PDAUG_Sequence_Property_Based_Descriptors.xml @ 10:187c6f2d3b55 draft default tip
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author | jay |
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date | Wed, 12 Jan 2022 20:20:40 +0000 |
parents | dd4523d4ae2f |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 <tool id="pdaug_sequence_property_based_descriptors" name="PDAUG Sequence Property Based Descriptors" version="0.1.0"> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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2 <description>Calculates sequence based descriptors of the peptide sequences</description> |
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3 |
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4 <requirements> |
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5 <requirement type="package" version="2.7.18">python</requirement> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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6 <requirement type="package" version="0.24.2">pandas</requirement> |
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7 <requirement type="package" version="1.0">pydpi</requirement> |
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8 </requirements> |
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9 |
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10 <command detect_errors="exit_code"><![CDATA[ |
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11 |
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12 python '$__tool_directory__/PDAUG_Sequence_Property_Based_Descriptors.py' --InFile '$input1' |
6b6aec52638d
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14 --DesType '$SelectDiscriptor.DesType' |
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15 |
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17 #if $SelectDiscriptor.DesType == 'GetPAAC' |
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19 --Lamda '$SelectDiscriptor.Lamda' |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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20 --Weight '$SelectDiscriptor.Weight' |
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21 |
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22 #end if |
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23 |
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24 |
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25 #if $SelectDiscriptor.DesType == 'GetAPAAC' |
7dc979925e31
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27 --Lamda '$SelectDiscriptor.Lamda' |
6b6aec52638d
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28 --Weight '$SelectDiscriptor.Weight' |
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29 |
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30 #end if |
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31 |
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32 |
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33 #if $SelectDiscriptor.DesType == 'GetSOCN' |
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34 |
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35 --MaxLag '$SelectDiscriptor.MaxLag' |
7dc979925e31
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36 |
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37 #end if |
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38 |
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39 |
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40 #if $SelectDiscriptor.DesType =='GetQSO' |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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41 |
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42 --MaxLag '$SelectDiscriptor.MaxLag' |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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43 --Weight '$SelectDiscriptor.Weight' |
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44 |
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45 #end if |
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46 |
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47 |
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48 #if $SelectDiscriptor.DesType =='All' |
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49 |
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50 --MaxLag '$SelectDiscriptor.MaxLag' |
7dc979925e31
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51 --Weight '$SelectDiscriptor.Weight' |
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52 --Lamda '$SelectDiscriptor.Lamda' |
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53 |
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54 #end if |
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56 |
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57 |
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58 -O '$output1' |
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59 |
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60 ]]></command> |
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61 |
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62 <inputs> |
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63 |
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64 <param name="input1" type="data" format="fasta" label="Input fasta file" help="Input fasta file with peptides"/> |
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65 |
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66 <conditional name="SelectDiscriptor"> |
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67 |
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68 <param name="DesType" type="select" label="Descriptor Type" argument=""> |
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69 <option value="GetAAComp">GetAAComp</option> |
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70 <option value="GetDPComp">GetDPComp</option> |
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71 <option value="GetTPComp" selected="true">GetTPComp</option> |
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72 <option value="GetMoreauBrotoAuto">GetMoreauBrotoAuto</option> |
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73 <option value="GetMoranAuto">GetMoranAuto</option> |
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74 <option value="GetGearyAuto">GetGearyAuto</option> |
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75 <option value="GetCTD">GetCTD</option> |
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76 <option value="GetPAAC">GetPAAC</option> |
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77 <option value="GetAPAAC">GetAPAAC</option> |
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78 <option value="GetSOCN">GetSOCN</option> |
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79 <option value="GetQSO">GetQSO</option> |
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80 <option value="GetTriad">GetTriad</option> |
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81 <option value="BinaryDescriptor">Binary Descriptor</option> |
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82 <option value="All">All</option> |
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83 </param> |
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84 |
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85 <when value="GetPAAC" > |
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86 <param name="Lamda" type="integer" label="Lamda" value="10" help="A non negative integer"/> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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87 <param name="Weight" type="float" label="Weight" value="0.5" help="Any value within the range from 0.05 to 0.7"/> |
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88 </when> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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89 |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
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|
90 <when value="GetAPAAC" > |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
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|
91 <param name="Lamda" type="integer" label="Lamda" value="10" help="A non negative integer"/> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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|
92 <param name="Weight" type="float" label="Weight" value="0.5" help="Any value within the range from 0.05 to 0.7"/> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
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|
93 </when> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
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|
94 |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
parents:
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|
95 <when value="GetQSO"> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
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|
96 <param name="MaxLag" type="integer" label="MaxLag" value="10" help="A non negative integer"/> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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|
97 <param name="Weight" type="float" label="Weight" value="0.5" help="Any value within the range from 0.05 to 0.7"/> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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|
98 </when> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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|
99 |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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100 <when value="GetSOCN"> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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101 <param name="MaxLag" type="integer" label="MaxLag" value="10" help="A non negative integer"/> |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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102 </when> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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103 |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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104 <when value="All" > |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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105 <param name="Lamda" type="integer" value="10" label="Lamda" help="A non negative integer"/> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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106 <param name="Weight" type="float" value="0.5" label="Weight" help="Weight"/> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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107 <param name="MaxLag" type="integer" value="10" label="Lamda" help="A non negative integer"/> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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108 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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109 |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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110 <when value="GetAAComp" > |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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111 </when> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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112 |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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113 <when value="GetDPComp" > |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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114 </when> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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115 |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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116 <when value="GetTPComp" > |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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117 </when> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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118 |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
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119 <when value="GetMoreauBrotoAuto" > |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
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120 </when> |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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121 |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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122 <when value="GetGearyAuto" > |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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123 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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124 |
5
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
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|
125 <when value="GetCTD" > |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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126 </when> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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127 |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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128 <when value="GetPAAC" > |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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129 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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130 |
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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131 <when value="GetAPAAC" > |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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132 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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133 |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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134 <when value="GetSOCN"> |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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135 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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136 |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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137 <when value="GetQSO"> |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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138 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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139 |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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140 <when value="GetTriad"> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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141 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
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142 |
6
dd4523d4ae2f
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit b929b576e510b09d0fed81103ca765b0ef669c30"
jay
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5
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|
143 <when value="GetMoranAuto" > |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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144 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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145 |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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146 <when value="BinaryDescriptor" > |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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147 </when> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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148 |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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149 </conditional> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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150 |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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151 </inputs> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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152 |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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153 <outputs> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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154 <data name='output1' format='tabular' label="${tool.name} on $on_string - ${SelectDiscriptor.DesType} (tabular)" /> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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155 </outputs> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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156 |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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157 <tests> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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158 <test> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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159 <param name="input1" value="positive.fasta"/> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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160 <param name="DesType" value="All"/> |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
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0
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|
161 <param name="Lamda" value="10"/> |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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162 <param name="Weight" value="0.5"/> |
5
7dc979925e31
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
jay
parents:
0
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|
163 <param name="MaxLag" value="10"/> |
0
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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|
164 <output name="output1" value="Out.tsv"/> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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|
165 </test> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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166 |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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167 |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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|
168 <test> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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|
169 <param name="input1" value="positive.fasta"/> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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|
170 <param name="DesType" value="BinaryDescriptor"/> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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|
171 <output name="output1" value="Out1.tsv"/> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
jay
parents:
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|
172 </test> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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173 |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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|
174 </tests> |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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parents:
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|
175 <help><![CDATA[ |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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|
176 .. class:: infomark |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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|
177 |
6b6aec52638d
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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|
178 **What it does** |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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179 |
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180 This tool calculates sequence property based descriptor for a peptide descriptor. |
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181 |
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182 * **GetAAComp** Amino acid compositon descriptors. |
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183 * **GetDPComp** Dipeptide composition descriptors. |
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184 * **GetTPComp** Tri-peptide composition descriptors. |
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185 * **GetMoreauBrotoAuto** Normalized Moreau-Broto autocorrelation descriptors. |
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186 * **GetMoranAuto** Moran autocorrelation descriptors. |
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187 * **GetGearyAuto** Geary autocorrelation descriptors. |
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188 * **GetCTD** Composition Transition Distribution descriptors. |
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189 * **GetPAAC** Type I Pseudo amino acid composition descriptors. |
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190 * **GetAPAAC** Amphiphilic (Type II) Pseudo amino acid composition descriptors. |
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191 * **GetSOCN** Sequence order coupling numbers. |
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192 * **GetQSO** Quasi sequence order descriptors default is 10, maxlag is the maximum lag. (The length of the protein should be larger than maxlag). |
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193 * **GetTriad** Calculate the conjoint triad features from the protein sequence. |
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194 * **Binary Descriptors** Calculate the conjoint triad features from the protein sequence. |
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195 * **All** Calculates all the available descriptors except binary. |
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196 |
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197 **Inputes** |
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198 |
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199 * **Input fasta file** Fasta file with peptide sequences. |
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200 * **Lamda** lamda reflects the rank of correlation, must be a non-Negative integer. Lamda should NOT be larger than the length of the input protein sequence. |
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201 * **Weight** weight is designed for the users to put weight on the additional PseAA components. Any value within the range from 0.05 to 0.7 for the weight factor can be used. |
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202 * **Maxlag** maxlag is the maximum lag. a non negative integer. The length of the protein should be larger than maxlag. |
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203 |
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204 ----- |
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205 |
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206 **Outputs** |
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207 * Returns tabular file with descriptors. |
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208 |
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209 ]]></help> |
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210 |
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211 <citations> |
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212 <citation type="bibtex"> |
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213 @misc{PDAUGGITHUB, |
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214 author = {Joshi, Jayadev and Blankenberg, Daniel}, |
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215 year = {2020}, |
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216 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, |
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217 publisher = {GitHub}, |
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218 journal = {GitHub repository}, |
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219 url = |
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220 {https://github.com/jaidevjoshi83/pdaug.git}, |
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221 } |
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222 </citation> |
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223 <citation type="bibtex"> |
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224 @article{cao_liang_yan_tan_xu_liu_2013, |
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225 title={PyDPI: Freely Available Python Package for Chemoinformatics, Bioinformatics, and Chemogenomics Studies}, |
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226 volume={53}, DOI={10.1021/ci400127q}, |
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227 number={11}, |
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228 journal={Journal of Chemical Information and Modeling}, |
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229 author={Cao, Dong-Sheng and Liang, Yi-Zeng and Yan, Jun and Tan, Gui-Shan and Xu, Qing-Song and Liu, Shao}, |
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230 year={2013}, |
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231 pages={3086–3096}} |
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232 </citation> |
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233 </citations> |
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234 </tool> |
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235 |
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236 |
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237 |