Mercurial > repos > anmoljh > padel_descriptor_calculation

annotate PaDEL-descriptor.xml @ 2:d35153edd310 draft default tip

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planemo upload commit 14622cfccfaec931b5937c5172d661de0ed69861-dirty
author anmoljh
date Tue, 05 Jun 2018 04:04:15 -0400
parents 3353a360ee1d
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1 <tool id="padel_descriptor" name="PaDEL-descriptor" version="1.0">
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2 <requirements>
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3 <requirement type="package" version="1.0">padeldescriptor</requirement>
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4 </requirements>
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5 <stdio>
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6 <exit_code range="1:" />
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7 </stdio>
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8
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9 <description>calculates descriptors for active and inactive datasets</description>
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10
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11 <command><![CDATA[
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12
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13 #if '.smi' in $input.name
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14 /bin/mkdir -p $input.extra_files_path;
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15 ln -sf $input $input.extra_files_path/molecule.smi;
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16 /usr/bin/java -jar \$PADELPATH/PaDEL-Descriptor.jar
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17 -dir $input.extra_files_path/molecule.smi
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18 $coordinate2d
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19 -maxruntime $maxruntime
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20 -waitingjobs $maxjob
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21 -threads $thread
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22 $detectaromaticity
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23 $removesalt
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24 $standardizenitro
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25 $convert3d
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26 $retain3d
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27 $coordinate3d
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28 $fingerprint
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29 $retainorder
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30 -file $descriptor -log > $log;
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31 /bin/rm -rf $input.extra_files_path;
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32 #else
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33 /usr/bin/java -jar \$PADELPATH/PaDEL-Descriptor.jar
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34 -dir $input
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35 $coordinate2d
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36 -maxruntime $maxruntime
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37 -waitingjobs $maxjob
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38 -threads $thread
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39 $detectaromaticity
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40 $removesalt
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41 $standardizenitro
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42 $convert3d
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43 $retain3d
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44 $coordinate3d
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45 $fingerprint
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46 $retainorder
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47 -file $descriptor -log > $log;
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48 #end if
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49
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50 ]]></command>
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51
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52 <inputs>
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53 <param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/>
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54
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55 <param name="detectaromaticity" type="select" label="Detect the aroamaticity">
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56 <option value="-detectaromaticity" selected="True">YES</option>
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57 <option value="" >NO</option>
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58 </param>
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59
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60 <param name="removesalt" type="select" label="Remove salt">
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61 <option value="-removesalt" selected="True">YES</option>
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62 <option value="">NO</option>
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63 </param>
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64
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65 <param name="standardizenitro" type="select" label="Standardize nitro groups">
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66 <option value="-standardizenitro" selected="True" >YES</option>
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67 <option value="">NO</option>
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68 </param>
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69
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70 <param name="maxruntime" type="integer" value="300000" label="Set run time for individual molecule" help="In miliseconds" >
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71 <validator type="empty_field" message="This field can't be left blank"/>
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72 </param>
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73
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74 <param name="thread" type="integer" value="8" label="Workers for the job" help="Set number of threads. -1 for maximun " >
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75 <validator type="empty_field" message="This field can't be left blank"/>
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76 </param>
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77
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78 <param name="maxjob" type="integer" value="-1" label="Maximum waiting job per thread. " help="Put -1 for maximum uitility or put positive inetger values upto 50" >
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79 <validator type="empty_field" message="This field can't be left blank"/>
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80 </param>
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81
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82 <param name="convert3d" type="select" label="convert in 3D">
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83 <option value="" selected="True">NO</option>
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84 <option value="-convert3d">YES</option>
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85 </param>
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86
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87 <param name="retain3d" type="select" label="Retain 3D coordinates">
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88 <option value="" selected="True">NO</option>
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89 <option value="-retain3d">YES</option>
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90 </param>
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91 <param name="coordinate2d" type="select" label="calculate 2d descriptors">
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92 <option value="">NO</option>
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93 <option value="-2d" selected="True">YES</option>
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94 </param>
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95
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96 <param name="coordinate3d" type="select" label="calculate 3d descriptors">
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97 <option value="" selected="True">NO</option>
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98 <option value="-3d">YES</option>
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99 </param>
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100
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101 <param name="fingerprint" type="select" label="calculate fingerprints">
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102 <option value="" selected="True">NO</option>
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103 <option value="-fingerprints">YES</option>
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104 </param>
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105
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106 <param name="retainorder" type="select" label="Retain molecules order">
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107 <option value="-retainorder" selected="True">YES</option>
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108 <option value="">NO</option>
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109 </param>
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110
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111 <!--
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112 <param name="3d" type="checkbox" label="Include 3D descriptors" description="add 3D descriptor" value="1" default="0" />
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113 <param name="fingerprint" type="checkbox" label="Include PubChem fingerprints" description="calculate 881 fingerprints" value="1" default="0" / >
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114 -->
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115 </inputs>
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116
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117 <outputs>
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118 <data format="csv" name="descriptor" label="Descriptors File of $input.name "/>
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119 <data format="txt" name="log" label="Log File of $input.name"/>
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120 </outputs>
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121
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122 <tests>
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123 <test>
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124 <param name="input" value="test.sdf" />
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125 <param name="detectaromaticity" value="-detectaromaticity" />
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126 <param name="removesalt" value="-removesalt" />
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127 <param name="standardizenitro" value="-standardizenitro" />
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128 <param name="convert3d" value="" />
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129 <param name="retain3d" value="-retain3d" />
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130 <param name="threads" value="8" />
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131 <param name="maxjob" value="8" />
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132 <param name="maxruntime" value="300000" />
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133 <param name="coordinate2d" value="-2d" />
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134 <param name="coordinate3d" value="-3d" />
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135 <param name="fingerprint" value="-fingerprints" />
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136 <param name="retainorder" value="-retainorder" />
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137 <output name="descriptor" file="descriptorfile.csv" compare="sim_size" delta="2000" />
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138 <output name="log" file="logs" compare="sim_size" delta="2000" />
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139 </test>
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140 </tests>
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141
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142 <help>Input may be any sdf,smile or mol2 file and output file will be in CSV format.</help>
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143
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144 </tool>