Mercurial > repos > deepakjadmin > padel_descriptors_test1

comparison padelnew.xml @ 19:79ae5df9a27e draft default tip

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author deepakjadmin
date Thu, 07 Jan 2016 01:23:21 -0500
parents 8feda385397b
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18:504061c1f812 19:79ae5df9a27e
9 <description>"PaDEL Descriptor Calculation Tool"</description> 9 <description>"PaDEL Descriptor Calculation Tool"</description>
10 <command interpreter=""> 10 <command interpreter="">
11 #if '.smi' in $input.name 11 #if '.smi' in $input.name
12 /bin/mkdir $input.extra_files_path; 12 /bin/mkdir $input.extra_files_path;
13 ln -s $input $input.extra_files_path/molecule.smi; 13 ln -s $input $input.extra_files_path/molecule.smi;
14 /usr/bin/java -jar \$PADEL_PATH/testpadel/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log > $log ; 14 /usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input.extra_files_path/molecule.smi -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log > $log ;
15 /bin/rm -rf $input.extra_files_path; 15 /bin/rm -rf $input.extra_files_path;
16 #else 16 #else
17 /usr/bin/java -jar \$PADEL_PATH/testpadel/PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log >$log 17 /usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input -2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate $fingerprint $retainorder -file $descriptor -log >$log
18 #end if 18 #end if
19 </command> 19 </command>
20 20
21 <inputs> 21 <inputs>
22 <param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/> 22 <param format="sdf" name="input" type="data" label="sdf/smile/mol2 file" optional= "false"/>