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comparison PaDEL-descriptor.xml @ 0:3353a360ee1d draft

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planemo upload commit a1f4dd8eb560c649391ada1a6bb9505893a35272
author anmoljh
date Thu, 31 May 2018 10:51:52 -0400
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children d35153edd310
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1 <tool id="padel_descriptor" name="PaDEL-descriptor" version="1.0">
2 <requirements>
3 <requirement type="package" version="1.0">padeldescriptor</requirement>
4 </requirements>
5 <stdio>
6 <exit_code range="1:" />
7 </stdio>
8
9 <description>"PaDEL Descriptor Calculation Tool"</description>
10
11 <command><![CDATA[
12
13 #if '.smi' in $input.name
14 /bin/mkdir -p $input.extra_files_path;
15 ln -sf $input $input.extra_files_path/molecule.smi;
16 /usr/bin/java -jar \$PADELPATH/PaDEL-Descriptor.jar
17 -dir $input.extra_files_path/molecule.smi
18 $coordinate2d
19 -maxruntime $maxruntime
20 -waitingjobs $maxjob
21 -threads $thread
22 $detectaromaticity
23 $removesalt
24 $standardizenitro
25 $convert3d
26 $retain3d
27 $coordinate3d
28 $fingerprint
29 $retainorder
30 -file $descriptor -log > $log;
31 /bin/rm -rf $input.extra_files_path;
32 #else
33 /usr/bin/java -jar \$PADELPATH/PaDEL-Descriptor.jar
34 -dir $input
35 $coordinate2d
36 -maxruntime $maxruntime
37 -waitingjobs $maxjob
38 -threads $thread
39 $detectaromaticity
40 $removesalt
41 $standardizenitro
42 $convert3d
43 $retain3d
44 $coordinate3d
45 $fingerprint
46 $retainorder
47 -file $descriptor -log > $log;
48 #end if
49
50 ]]></command>
51
52 <inputs>
53 <param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/>
54
55 <param name="detectaromaticity" type="select" label="Detect the aroamaticity">
56 <option value="-detectaromaticity" selected="True">YES</option>
57 <option value="" >NO</option>
58 </param>
59
60 <param name="removesalt" type="select" label="Remove salt">
61 <option value="-removesalt" selected="True">YES</option>
62 <option value="">NO</option>
63 </param>
64
65 <param name="standardizenitro" type="select" label="Standardize nitro groups">
66 <option value="-standardizenitro" selected="True" >YES</option>
67 <option value="">NO</option>
68 </param>
69
70 <param name="maxruntime" type="integer" value="300000" label="Set run time for individual molecule" help="In miliseconds" >
71 <validator type="empty_field" message="This field can't be left blank"/>
72 </param>
73
74 <param name="thread" type="integer" value="8" label="Workers for the job" help="Set number of threads. -1 for maximun " >
75 <validator type="empty_field" message="This field can't be left blank"/>
76 </param>
77
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" >
79 <validator type="empty_field" message="This field can't be left blank"/>
80 </param>
81
82 <param name="convert3d" type="select" label="convert in 3D">
83 <option value="" selected="True">NO</option>
84 <option value="-convert3d">YES</option>
85 </param>
86
87 <param name="retain3d" type="select" label="Retain 3D coordinates">
88 <option value="" selected="True">NO</option>
89 <option value="-retain3d">YES</option>
90 </param>
91 <param name="coordinate2d" type="select" label="calculate 2d descriptors">
92 <option value="">NO</option>
93 <option value="-2d" selected="True">YES</option>
94 </param>
95
96 <param name="coordinate3d" type="select" label="calculate 3d descriptors">
97 <option value="" selected="True">NO</option>
98 <option value="-3d">YES</option>
99 </param>
100
101 <param name="fingerprint" type="select" label="calculate fingerprints">
102 <option value="" selected="True">NO</option>
103 <option value="-fingerprints">YES</option>
104 </param>
105
106 <param name="retainorder" type="select" label="Retain molecules order">
107 <option value="-retainorder" selected="True">YES</option>
108 <option value="">NO</option>
109 </param>
110
111 <!--
112 <param name="3d" type="checkbox" label="Include 3D descriptors" description="add 3D descriptor" value="1" default="0" />
113 <param name="fingerprint" type="checkbox" label="Include PubChem fingerprints" description="calculate 881 fingerprints" value="1" default="0" / >
114 -->
115 </inputs>
116
117 <outputs>
118 <data format="csv" name="descriptor" label="Descriptors File of $input.name "/>
119 <data format="txt" name="log" label="Log File of $input.name"/>
120 </outputs>
121
122 <tests>
123 <test>
124 <param name="input" value="test.sdf" />
125 <param name="detectaromaticity" value="-detectaromaticity" />
126 <param name="removesalt" value="-removesalt" />
127 <param name="standardizenitro" value="-standardizenitro" />
128 <param name="convert3d" value="" />
129 <param name="retain3d" value="-retain3d" />
130 <param name="threads" value="8" />
131 <param name="maxjob" value="8" />
132 <param name="maxruntime" value="300000" />
133 <param name="coordinate2d" value="-2d" />
134 <param name="coordinate3d" value="-3d" />
135 <param name="fingerprint" value="-fingerprints" />
136 <param name="retainorder" value="-retainorder" />
137 <output name="descriptor" file="descriptorfile.csv" compare="sim_size" delta="2000" />
138 <output name="log" file="logs" compare="sim_size" delta="2000" />
139 </test>
140 </tests>
141
142 <help>Input may be any sdf,smile or mol2 file and output file will be in CSV format.</help>
143
144 </tool>