Mercurial > repos > deepakjadmin > padel_descriptors_test5

comparison padelnew.xml @ 2:24364e0f3b2c draft default tip

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author deepakjadmin
date Fri, 30 Dec 2016 03:12:08 -0500
parents e22b7430ba3a
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1:e22b7430ba3a 2:24364e0f3b2c
8 <description>"PaDEL Descriptor Calculation Tool"</description> 8 <description>"PaDEL Descriptor Calculation Tool"</description>
9 <command interpreter=""> 9 <command interpreter="">
10 #if '.smi' in $input.name 10 #if '.smi' in $input.name
11 /bin/mkdir $input.extra_files_path; 11 /bin/mkdir $input.extra_files_path;
12 ln -s $input $input.extra_files_path/molecule.smi; 12 ln -s $input $input.extra_files_path/molecule.smi;
13 /usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi $coordinate2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d $fingerprint $retainorder -file $descriptor -log > $log ; 13 /usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi $coordinate2d -maxruntime $maxruntime -waitingjobs $maxjob -threads $thread-$detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d $fingerprint $retainorder -file $descriptor -log > $log ;
14 /bin/rm -rf $input.extra_files_path; 14 /bin/rm -rf $input.extra_files_path;
15 #else 15 #else
16 /usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input $coordinate2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d $fingerprint $retainorder -file $descriptor -log >$log 16 /usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input $coordinate2d -maxruntime $maxruntime -waitingjobs $maxjob -threads $thread $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d $fingerprint $retainorder -file $descriptor -log >$log
17 #end if 17 #end if
18 </command> 18 </command>
19 19
20 <inputs> 20 <inputs>
21 <param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/> 21 <param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/>
32 32
33 <param name="standardizenitro" type="select" label="Standardize nitro groups"> 33 <param name="standardizenitro" type="select" label="Standardize nitro groups">
34 <option value = "-standardizenitro" selected="TRUE" >YES</option> 34 <option value = "-standardizenitro" selected="TRUE" >YES</option>
35 <option value = "" >NO</option> 35 <option value = "" >NO</option>
36 </param> 36 </param>
37
38 <param name="maxruntime" type="integer" value="300000" label="Set run time for individual molecule" help="in miliseconds" >
39 <validator type="empty_field" message="This field can't be left blank"/>
40 </param>
41
42 <param name="thread" type="integer" value="8" label="Workers for the job" help="set number of threads -1 for maximun " >
43 <validator type="empty_field" message="This field can't be left blank"/>
44 </param>
45
46
47 <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" >
48 <validator type="empty_field" message="This field can't be left blank"/>
49 </param>
50
37 51
38 <param name="convert3d" type="select" label="convert in 3D"> 52 <param name="convert3d" type="select" label="convert in 3D">
39 <option value = "" selected="TRUE" >NO</option> 53 <option value = "" selected="TRUE" >NO</option>
40 <option value = "-convert3d" >YES</option> 54 <option value = "-convert3d" >YES</option>
41 </param> 55 </param>
42 56
57
58
43 <param name="retain3d" type="select" label="Retain 3D coordinates"> 59 <param name="retain3d" type="select" label="Retain 3D coordinates">
44 <option value = "" selected="TRUE" >NO</option> 60 <option value = "" selected="TRUE" >NO</option>
45 <option value = "-retain3d" >YES</option> 61 <option value = "-retain3d" >YES</option>
62
46 63
47 </param> 64 </param>
48 65
49 <param name="coordinate3d" type="select" label="calculate 3d descriptors"> 66 <param name="coordinate3d" type="select" label="calculate 3d descriptors">
50 <option value = "" selected="TRUE" >NO</option> 67 <option value = "" selected="TRUE" >NO</option>