Mercurial > repos > deepakjadmin > padel_descriptors_test5
changeset 2:24364e0f3b2c draft default tip
Uploaded
author | deepakjadmin |
---|---|
date | Fri, 30 Dec 2016 03:12:08 -0500 |
parents | e22b7430ba3a |
children | |
files | padelnew.xml |
diffstat | 1 files changed, 19 insertions(+), 2 deletions(-) [+] |
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line diff
--- a/padelnew.xml Sat Dec 24 11:40:35 2016 -0500 +++ b/padelnew.xml Fri Dec 30 03:12:08 2016 -0500 @@ -10,10 +10,10 @@ #if '.smi' in $input.name /bin/mkdir $input.extra_files_path; ln -s $input $input.extra_files_path/molecule.smi; -/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 ; +/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 ; /bin/rm -rf $input.extra_files_path; #else -/usr/bin/java -jar \$PADEL_PATH/PaDEL-Descriptor.jar -dir $input $coordinate2d $detectaromaticity $removesalt $standardizenitro $convert3d $retain3d $coordinate3d $fingerprint $retainorder -file $descriptor -log >$log +/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 #end if </command> @@ -34,15 +34,32 @@ <option value = "-standardizenitro" selected="TRUE" >YES</option> <option value = "" >NO</option> </param> + + <param name="maxruntime" type="integer" value="300000" label="Set run time for individual molecule" help="in miliseconds" > + <validator type="empty_field" message="This field can't be left blank"/> + </param> + + <param name="thread" type="integer" value="8" label="Workers for the job" help="set number of threads -1 for maximun " > + <validator type="empty_field" message="This field can't be left blank"/> + </param> + + + <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" > + <validator type="empty_field" message="This field can't be left blank"/> + </param> + <param name="convert3d" type="select" label="convert in 3D"> <option value = "" selected="TRUE" >NO</option> <option value = "-convert3d" >YES</option> </param> + + <param name="retain3d" type="select" label="Retain 3D coordinates"> <option value = "" selected="TRUE" >NO</option> <option value = "-retain3d" >YES</option> + </param>